Read the Docs build information
Build id: 224457
Project: cyverse-container-camp-workshop-2019
Version: latest
Commit: 5d193f47bac4371a2b15b6933ceb532b547854de
Date: 2019-07-17T18:00:17.088467Z
State: finished
Success: True


[rtd-command-info] start-time: 2019-07-17T18:00:17.829246Z, end-time: 2019-07-17T18:00:17.852882Z, duration: 0, exit-code: 0
git remote set-url origin https://github.com/CyVerse-learning-materials/container_camp_workshop_2019.git


[rtd-command-info] start-time: 2019-07-17T18:00:17.932709Z, end-time: 2019-07-17T18:00:19.200186Z, duration: 1, exit-code: 0
git fetch --tags --prune --prune-tags --depth 50
From https://github.com/CyVerse-learning-materials/container_camp_workshop_2019
   dfccc5e..5d193f4  master     -> origin/master

[rtd-command-info] start-time: 2019-07-17T18:00:19.441926Z, end-time: 2019-07-17T18:00:19.590723Z, duration: 0, exit-code: 0
git checkout --force origin/master
Previous HEAD position was dfccc5e Merge pull request #5 from sanjanasudarshan/master
HEAD is now at 5d193f4 Merge pull request #6 from sanjanasudarshan/master

[rtd-command-info] start-time: 2019-07-17T18:00:19.674881Z, end-time: 2019-07-17T18:00:19.701563Z, duration: 0, exit-code: 0
git clean -d -f -f
Removing misc/__init__.pyc
Removing misc/cyverse_sphinx_conf.pyc

[rtd-command-info] start-time: 2019-07-17T18:00:21.451875Z, end-time: 2019-07-17T18:00:24.721553Z, duration: 3, exit-code: 0
python2.7 -mvirtualenv --no-site-packages --no-download 
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/bin/python2.7
Not overwriting existing python script /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/bin/python (you must use /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/bin/python2.7)
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2019-07-17T18:00:24.845525Z, end-time: 2019-07-17T18:00:25.867162Z, duration: 1, exit-code: 0
python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/.cache/pip pip
Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (19.1.1)

[rtd-command-info] start-time: 2019-07-17T18:00:25.955329Z, end-time: 2019-07-17T18:00:28.088417Z, duration: 2, exit-code: 0
python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/.cache/pip Pygments==2.3.1 setuptools==41.0.1 docutils==0.14 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<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<0.6
Requirement already up-to-date: Pygments==2.3.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (2.3.1)
Requirement already up-to-date: setuptools==41.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (41.0.1)
Requirement already up-to-date: docutils==0.14 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (0.14)
Requirement already up-to-date: mock==1.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (1.0.1)
Requirement already up-to-date: pillow==5.4.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (5.4.1)
Requirement already up-to-date: alabaster!=0.7.5,<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (0.7.12)
Requirement already up-to-date: commonmark==0.8.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (0.8.1)
Requirement already up-to-date: recommonmark==0.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (0.5.0)
Requirement already up-to-date: sphinx<2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (1.8.5)
Requirement already up-to-date: sphinx-rtd-theme<0.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (0.4.3)
Requirement already up-to-date: readthedocs-sphinx-ext<0.6 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (0.5.17)
Requirement already satisfied, skipping upgrade: future in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from commonmark==0.8.1) (0.17.1)
Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx<2) (1.9.0)
Requirement already satisfied, skipping upgrade: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx<2) (1.1.2)
Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx<2) (2.7.0)
Requirement already satisfied, skipping upgrade: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx<2) (2.22.0)
Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx<2) (2.10.1)
Requirement already satisfied, skipping upgrade: packaging in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx<2) (19.0)
Requirement already satisfied, skipping upgrade: typing; python_version < "3.5" in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx<2) (3.7.4)
Requirement already satisfied, skipping upgrade: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx<2) (1.1.0)
Requirement already satisfied, skipping upgrade: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx<2) (1.12.0)
Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from babel!=2.0,>=1.3->sphinx<2) (2019.1)
Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx<2) (1.25.3)
Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx<2) (2019.6.16)
Requirement already satisfied, skipping upgrade: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx<2) (3.0.4)
Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx<2) (2.8)
Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from Jinja2>=2.3->sphinx<2) (1.1.1)
Requirement already satisfied, skipping upgrade: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from packaging->sphinx<2) (2.4.0)

[rtd-command-info] start-time: 2019-07-17T18:00:28.165117Z, end-time: 2019-07-17T18:00:29.015936Z, duration: 0, exit-code: 0
python -m pip install --exists-action=w --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/.cache/pip -r requirements.txt
Requirement already satisfied: sphinx in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from -r requirements.txt (line 1)) (1.8.5)
Requirement already satisfied: recommonmark in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from -r requirements.txt (line 2)) (0.5.0)
Requirement already satisfied: sphinxcontrib-images in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from -r requirements.txt (line 3)) (0.8.0)
Requirement already satisfied: sphinx_bootstrap_theme in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from -r requirements.txt (line 4)) (0.7.1)
Requirement already satisfied: guzzle_sphinx_theme==0.7.11 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from -r requirements.txt (line 5)) (0.7.11)
Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (0.7.12)
Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (1.9.0)
Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (2.3.1)
Requirement already satisfied: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (1.1.2)
Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (19.0)
Requirement already satisfied: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (2.7.0)
Requirement already satisfied: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (2.22.0)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (41.0.1)
Requirement already satisfied: docutils>=0.11 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (0.14)
Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (2.10.1)
Requirement already satisfied: typing; python_version < "3.5" in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (3.7.4)
Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (1.1.0)
Requirement already satisfied: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from sphinx->-r requirements.txt (line 1)) (1.12.0)
Requirement already satisfied: commonmark>=0.7.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from recommonmark->-r requirements.txt (line 2)) (0.8.1)
Requirement already satisfied: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from packaging->sphinx->-r requirements.txt (line 1)) (2.4.0)
Requirement already satisfied: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from babel!=2.0,>=1.3->sphinx->-r requirements.txt (line 1)) (2019.1)
Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx->-r requirements.txt (line 1)) (1.25.3)
Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx->-r requirements.txt (line 1)) (2019.6.16)
Requirement already satisfied: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx->-r requirements.txt (line 1)) (3.0.4)
Requirement already satisfied: idna<2.9,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx->-r requirements.txt (line 1)) (2.8)
Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from Jinja2>=2.3->sphinx->-r requirements.txt (line 1)) (1.1.1)
Requirement already satisfied: future in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (from commonmark>=0.7.3->recommonmark->-r requirements.txt (line 2)) (0.17.1)

[rtd-command-info] start-time: 2019-07-17T18:00:29.713459Z, end-time: 2019-07-17T18:00:30.040498Z, duration: 0, exit-code: 0
cat conf.py
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# General information about the project.

import sys
import os
sys.path.insert(0, os.path.dirname(__file__))

from misc.cyverse_sphinx_conf import *  # noqa

project = 'CyVerse Container Camp 2019'
copyright = '2019, CyVerse'
author = 'CyVerse'

epub_title = project
epub_author = author
epub_publisher = author
epub_copyright = copyright




###########################################################################
#          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/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl
#


import importlib
import sys
import os.path
from six import string_types

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 mulitple 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://media.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://media.readthedocs.com/",
    'PRODUCTION_DOMAIN': "readthedocs.com",
    'versions': [
    ("latest", "/en/latest/"),
    ],
    'downloads': [ 
    ("pdf", "//readthedocs.com/projects/cyverse-container-camp-workshop-2019/downloads/pdf/latest/"),
    ("html", "//readthedocs.com/projects/cyverse-container-camp-workshop-2019/downloads/htmlzip/latest/"),
    ("epub", "//readthedocs.com/projects/cyverse-container-camp-workshop-2019/downloads/epub/latest/"),
    ],
    'subprojects': [ 
    ],
    'slug': 'cyverse-container-camp-workshop-2019',
    'name': u'container_camp_workshop_2019',
    'rtd_language': u'en',
    'programming_language': u'words',
    'canonical_url': 'https://learning.cyverse.org/projects/container_camp_workshop_2019/en/latest/',
    'analytics_code': 'None',
    'single_version': False,
    'conf_py_path': '/',
    'api_host': 'https://readthedocs.com',
    'github_user': 'CyVerse-learning-materials',
    'github_repo': 'container_camp_workshop_2019',
    '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,
    'user_analytics_code': '',
    'global_analytics_code': 'UA-17997319-2',
    'commit': '5d193f47',
}




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"]

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'

[rtd-command-info] start-time: 2019-07-17T18:00:30.157290Z, end-time: 2019-07-17T18:00:43.004143Z, duration: 12, exit-code: 0
python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
Running Sphinx v1.8.5
loading translations [en]... done
making output directory...
building [mo]: targets for 0 po files that are out of date
building [readthedocs]: targets for 55 source files that are out of date
updating environment: 55 added, 0 changed, 0 removed
reading sources... [  1%] breakout/biocontainers
reading sources... [  3%] breakout/datascience
reading sources... [  5%] breakout/nvidia-docker
reading sources... [  7%] breakout/workflows
reading sources... [  9%] buildenv/lib/python3.5/site-packages/Babel-2.5.3.dist-info/DESCRIPTION
reading sources... [ 10%] buildenv/lib/python3.5/site-packages/CommonMark-0.5.4.dist-info/DESCRIPTION
reading sources... [ 12%] buildenv/lib/python3.5/site-packages/Jinja2-2.10.dist-info/DESCRIPTION
reading sources... [ 14%] buildenv/lib/python3.5/site-packages/MarkupSafe-1.0.dist-info/DESCRIPTION
reading sources... [ 16%] buildenv/lib/python3.5/site-packages/Pygments-2.2.0.dist-info/DESCRIPTION
reading sources... [ 18%] buildenv/lib/python3.5/site-packages/Sphinx-1.6.6.dist-info/DESCRIPTION
reading sources... [ 20%] buildenv/lib/python3.5/site-packages/alabaster-0.7.10.dist-info/DESCRIPTION
reading sources... [ 21%] buildenv/lib/python3.5/site-packages/certifi-2018.1.18.dist-info/DESCRIPTION
reading sources... [ 23%] buildenv/lib/python3.5/site-packages/chardet-3.0.4.dist-info/DESCRIPTION
reading sources... [ 25%] buildenv/lib/python3.5/site-packages/docutils-0.14.dist-info/DESCRIPTION
reading sources... [ 27%] buildenv/lib/python3.5/site-packages/guzzle_sphinx_theme-0.7.11.dist-info/DESCRIPTION
reading sources... [ 29%] buildenv/lib/python3.5/site-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/README
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages/recommonmark/parser.py:65: UserWarning: Container node skipped: type=document
  warn("Container node skipped: type={0}".format(mdnode.t))
reading sources... [ 30%] buildenv/lib/python3.5/site-packages/idna-2.6.dist-info/DESCRIPTION
reading sources... [ 32%] buildenv/lib/python3.5/site-packages/imagesize-0.7.1.dist-info/DESCRIPTION
reading sources... [ 34%] buildenv/lib/python3.5/site-packages/pip-9.0.1.dist-info/DESCRIPTION
reading sources... [ 36%] buildenv/lib/python3.5/site-packages/pytz-2017.3.dist-info/DESCRIPTION
reading sources... [ 38%] buildenv/lib/python3.5/site-packages/recommonmark-0.4.0.dist-info/DESCRIPTION
reading sources... [ 40%] buildenv/lib/python3.5/site-packages/requests-2.18.4.dist-info/DESCRIPTION
reading sources... [ 41%] buildenv/lib/python3.5/site-packages/setuptools-38.4.0.dist-info/DESCRIPTION
reading sources... [ 43%] buildenv/lib/python3.5/site-packages/six-1.11.0.dist-info/DESCRIPTION
reading sources... [ 45%] buildenv/lib/python3.5/site-packages/snowballstemmer-1.2.1.dist-info/DESCRIPTION
reading sources... [ 47%] buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/base
reading sources... [ 49%] buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/class
reading sources... [ 50%] buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/module
reading sources... [ 52%] buildenv/lib/python3.5/site-packages/sphinx_bootstrap_theme-0.6.4.dist-info/DESCRIPTION
reading sources... [ 54%] buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/DESCRIPTION
reading sources... [ 56%] buildenv/lib/python3.5/site-packages/sphinxcontrib_images-0.7.0.dist-info/DESCRIPTION
reading sources... [ 58%] buildenv/lib/python3.5/site-packages/sphinxcontrib_websupport-1.0.1.dist-info/DESCRIPTION
reading sources... [ 60%] buildenv/lib/python3.5/site-packages/urllib3-1.22.dist-info/DESCRIPTION
reading sources... [ 61%] buildenv/lib/python3.5/site-packages/wheel-0.30.0.dist-info/DESCRIPTION
reading sources... [ 63%] cyverse/boot
reading sources... [ 65%] cyverse/de_docker
reading sources... [ 67%] cyverse/vice_docker
reading sources... [ 69%] docker/dockeradvanced
reading sources... [ 70%] docker/dockerhandson
reading sources... [ 72%] docker/dockerintro
reading sources... [ 74%] getting_started/about_cyverse
reading sources... [ 76%] getting_started/agenda
reading sources... [ 78%] getting_started/installation
reading sources... [ 80%] getting_started/main
reading sources... [ 81%] index
reading sources... [ 83%] instructions_reporting/instructors
reading sources... [ 85%] instructions_reporting/problems
reading sources... [ 87%] singularity/singularityadvanced
reading sources... [ 89%] singularity/singularityintro
reading sources... [ 90%] topics/breakout_session
reading sources... [ 92%] topics/train_docker
reading sources... [ 94%] topics/train_singularity
reading sources... [ 96%] useful_resources/usefulresources_docker
reading sources... [ 98%] useful_resources/usefulresources_other
reading sources... [100%] useful_resources/usefulresources_singularity

/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/breakout/biocontainers.rst:2: WARNING: Title underline too short.

**Biocontainers**
================
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/breakout/datascience.rst:2: WARNING: Duplicate explicit target name: "here".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/requests-2.18.4.dist-info/DESCRIPTION.rst:162: WARNING: Inline emphasis start-string without end-string.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/base.rst:3: WARNING: Error in "currentmodule" directive:
maximum 1 argument(s) allowed, 3 supplied.

.. currentmodule:: {{ module }}
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/class.rst:3: WARNING: Error in "currentmodule" directive:
maximum 1 argument(s) allowed, 3 supplied.

.. currentmodule:: {{ module }}
WARNING: invalid signature for autoclass (u'{{ objname }}')
WARNING: don't know which module to import for autodocumenting u'{{ objname }}' (try placing a "module" or "currentmodule" directive in the document, or giving an explicit module name)
WARNING: invalid signature for automodule (u'{{ fullname }}')
WARNING: don't know which module to import for autodocumenting u'{{ fullname }}' (try placing a "module" or "currentmodule" directive in the document, or giving an explicit module name)
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/DESCRIPTION.rst:: WARNING: image file not readable: buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/screen_mobile.png
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/cyverse/boot.rst:70: WARNING: Content block expected for the "important" directive; none found.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/cyverse/de_docker.rst:4: WARNING: Duplicate explicit target name: "dockerhub".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/cyverse/vice_docker.rst:4: WARNING: Duplicate explicit target name: "here".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockeradvanced.rst:2: WARNING: Duplicate explicit target name: "docker hub".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockeradvanced.rst:441: WARNING: Error in "code-block" directive:
maximum 1 argument(s) allowed, 3 supplied.

.. code-block:: bash
   -v /home/username/your_data_folder:/data:ro
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockeradvanced.rst:527: WARNING: Error in "code-block" directive:
1 argument(s) required, 0 supplied.

.. code-block::

        HOSTNAME=790e13bba28a
        SHLVL=1
        HOME=/root
        PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
        PWD=/
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockerhandson.rst:35: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockerintro.rst:501: WARNING: Duplicate explicit target name: "dockerfile".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockerintro.rst:557: WARNING: Duplicate explicit target name: "build the image".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockerintro.rst:594: WARNING: Duplicate explicit target name: "run your image".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockerintro.rst:473: WARNING: Duplicate target name, cannot be used as a unique reference: "build the image".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockerintro.rst:474: WARNING: Duplicate target name, cannot be used as a unique reference: "run your image".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/getting_started/agenda.rst:2: WARNING: Duplicate explicit target name: "slides".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/getting_started/main.rst:4: WARNING: Title underline too short.

**Workshop Code of Conduct and Other Information**
============================
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityadvanced.rst:7: WARNING: Title underline too short.

5.0 Building your own Containers from scratch
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityadvanced.rst:30: WARNING: Title underline too short.

5.2 Building Singularity containers
==================================
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityadvanced.rst:74: WARNING: Title underline too short.

5.2.1: Exercise (~30 minutes): Create a Singularity file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityadvanced.rst:74: WARNING: Title underline too short.

5.2.1: Exercise (~30 minutes): Create a Singularity file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityadvanced.rst:140: WARNING: Duplicate explicit target name: "user guide".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityadvanced.rst:278: WARNING: Error in "code-block" directive:
maximum 1 argument(s) allowed, 7 supplied.

.. code-block:: bash
  BootStrap: debootstrap
  OSVersion: xenial
  MirrorURL: http://us.archive.ubuntu.com/ubuntu/

  %runscript
      echo "This is what happens when you run the container..."

  %post
      echo "Hello from inside the container"
      sed -i 's/$/ universe/' /etc/apt/sources.list
      apt update
      apt -y --allow-unauthenticated install vim build-essential wget gfortran bison libibverbs-dev libibmad-dev libibumad-dev librdmacm-dev libmlx5-dev libmlx4-dev
      wget http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.1.tar.gz
      tar xvf mvapich2-2.1.tar.gz
      cd mvapich2-2.1
      ./configure --prefix=/usr/local
      make -j4
      make install
      /usr/local/bin/mpicc examples/hellow.c -o /usr/bin/hellow
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityintro.rst:2: WARNING: Duplicate explicit target name: "singularity".
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/Babel-2.5.3.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/CommonMark-0.5.4.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/Jinja2-2.10.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/MarkupSafe-1.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/Pygments-2.2.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/Sphinx-1.6.6.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/alabaster-0.7.10.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/certifi-2018.1.18.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/chardet-3.0.4.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/docutils-0.14.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/guzzle_sphinx_theme-0.7.11.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/README.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/idna-2.6.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/imagesize-0.7.1.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/pip-9.0.1.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/pytz-2017.3.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/recommonmark-0.4.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/requests-2.18.4.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/setuptools-38.4.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/six-1.11.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/snowballstemmer-1.2.1.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/base.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/class.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/module.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx_bootstrap_theme-0.6.4.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinxcontrib_images-0.7.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinxcontrib_websupport-1.0.1.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/urllib3-1.22.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/wheel-0.30.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
done
preparing documents... done
writing output... [  1%] breakout/biocontainers
writing output... [  3%] breakout/datascience
writing output... [  5%] breakout/nvidia-docker
writing output... [  7%] breakout/workflows
writing output... [  9%] buildenv/lib/python3.5/site-packages/Babel-2.5.3.dist-info/DESCRIPTION
writing output... [ 10%] buildenv/lib/python3.5/site-packages/CommonMark-0.5.4.dist-info/DESCRIPTION
writing output... [ 12%] buildenv/lib/python3.5/site-packages/Jinja2-2.10.dist-info/DESCRIPTION
writing output... [ 14%] buildenv/lib/python3.5/site-packages/MarkupSafe-1.0.dist-info/DESCRIPTION
writing output... [ 16%] buildenv/lib/python3.5/site-packages/Pygments-2.2.0.dist-info/DESCRIPTION
writing output... [ 18%] buildenv/lib/python3.5/site-packages/Sphinx-1.6.6.dist-info/DESCRIPTION
writing output... [ 20%] buildenv/lib/python3.5/site-packages/alabaster-0.7.10.dist-info/DESCRIPTION
writing output... [ 21%] buildenv/lib/python3.5/site-packages/certifi-2018.1.18.dist-info/DESCRIPTION
writing output... [ 23%] buildenv/lib/python3.5/site-packages/chardet-3.0.4.dist-info/DESCRIPTION
writing output... [ 25%] buildenv/lib/python3.5/site-packages/docutils-0.14.dist-info/DESCRIPTION
writing output... [ 27%] buildenv/lib/python3.5/site-packages/guzzle_sphinx_theme-0.7.11.dist-info/DESCRIPTION
writing output... [ 29%] buildenv/lib/python3.5/site-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/README
writing output... [ 30%] buildenv/lib/python3.5/site-packages/idna-2.6.dist-info/DESCRIPTION
writing output... [ 32%] buildenv/lib/python3.5/site-packages/imagesize-0.7.1.dist-info/DESCRIPTION
writing output... [ 34%] buildenv/lib/python3.5/site-packages/pip-9.0.1.dist-info/DESCRIPTION
writing output... [ 36%] buildenv/lib/python3.5/site-packages/pytz-2017.3.dist-info/DESCRIPTION
writing output... [ 38%] buildenv/lib/python3.5/site-packages/recommonmark-0.4.0.dist-info/DESCRIPTION
writing output... [ 40%] buildenv/lib/python3.5/site-packages/requests-2.18.4.dist-info/DESCRIPTION
writing output... [ 41%] buildenv/lib/python3.5/site-packages/setuptools-38.4.0.dist-info/DESCRIPTION
writing output... [ 43%] buildenv/lib/python3.5/site-packages/six-1.11.0.dist-info/DESCRIPTION
writing output... [ 45%] buildenv/lib/python3.5/site-packages/snowballstemmer-1.2.1.dist-info/DESCRIPTION
writing output... [ 47%] buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/base
writing output... [ 49%] buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/class
writing output... [ 50%] buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/module
writing output... [ 52%] buildenv/lib/python3.5/site-packages/sphinx_bootstrap_theme-0.6.4.dist-info/DESCRIPTION
writing output... [ 54%] buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/DESCRIPTION
writing output... [ 56%] buildenv/lib/python3.5/site-packages/sphinxcontrib_images-0.7.0.dist-info/DESCRIPTION
writing output... [ 58%] buildenv/lib/python3.5/site-packages/sphinxcontrib_websupport-1.0.1.dist-info/DESCRIPTION
writing output... [ 60%] buildenv/lib/python3.5/site-packages/urllib3-1.22.dist-info/DESCRIPTION
writing output... [ 61%] buildenv/lib/python3.5/site-packages/wheel-0.30.0.dist-info/DESCRIPTION
writing output... [ 63%] cyverse/boot
writing output... [ 65%] cyverse/de_docker
writing output... [ 67%] cyverse/vice_docker
writing output... [ 69%] docker/dockeradvanced
writing output... [ 70%] docker/dockerhandson
writing output... [ 72%] docker/dockerintro
writing output... [ 74%] getting_started/about_cyverse
writing output... [ 76%] getting_started/agenda
writing output... [ 78%] getting_started/installation
writing output... [ 80%] getting_started/main
writing output... [ 81%] index
writing output... [ 83%] instructions_reporting/instructors
writing output... [ 85%] instructions_reporting/problems
writing output... [ 87%] singularity/singularityadvanced
writing output... [ 89%] singularity/singularityintro
writing output... [ 90%] topics/breakout_session
writing output... [ 92%] topics/train_docker
writing output... [ 94%] topics/train_singularity
writing output... [ 96%] useful_resources/usefulresources_docker
writing output... [ 98%] useful_resources/usefulresources_other
writing output... [100%] useful_resources/usefulresources_singularity

/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockeradvanced.rst:595: WARNING: Could not lex literal_block as "bash". Highlighting skipped.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityintro.rst:77: WARNING: Could not lex literal_block as "bash". Highlighting skipped.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityintro.rst:112: WARNING: Could not lex literal_block as "bash". Highlighting skipped.
generating indices... genindex
writing additional pages... search
copying images... [  1%] docker/../img/bind_mount.png
copying images... [  3%] cyverse/../img/atmo-8.png
copying images... [  4%] cyverse/../img/jupyter1-6.png
copying images... [  6%] cyverse/../img/atmo_launch0.png
copying images... [  7%] docker/../img/docker_image.png
copying images... [  9%] docker/../img/dc-1.png
copying images... [ 10%] breakout/../img/rstudio_login2.png
copying images... [ 12%] cyverse/../img/img_building_5.png
copying images... [ 13%] docker/../img/fastqe.png
copying images... [ 15%] cyverse/../img/auto-3.png
copying images... [ 16%] docker/../img/dockerhub_create.png
copying images... [ 18%] cyverse/../img/auto-4.png
copying images... [ 20%] breakout/../img/snakemake.png
copying images... [ 21%] cyverse/../img/atmo_launch.png
copying images... [ 23%] instructions_reporting/../img/static_site_docker.png
copying images... [ 24%] docker/../img/pwd.png
copying images... [ 26%] cyverse/../img/atmo-9.png
copying images... [ 27%] cyverse/../img/img_building_9.png
copying images... [ 29%] docker/../img/portainer_demo.png
copying images... [ 30%] cyverse/../img/img_building_3.png
copying images... [ 32%] cyverse/../img/img_building_1.png
copying images... [ 33%] breakout/../img/rstudio_ss.png
copying images... [ 35%] docker/../img/dockerhub_autobuild.png
copying images... [ 36%] cyverse/../img/auto-1.png
copying images... [ 38%] docker/../img/create_repo2.png
copying images... [ 40%] cyverse/../img/jupyter1-9.png
copying images... [ 41%] docker/../img/jn_login.png
copying images... [ 43%] cyverse/../img/atmo-1.1.png
copying images... [ 44%] cyverse/../img/cyverse_rgb.png
copying images... [ 46%] ./img/cc-main.png
copying images... [ 47%] breakout/../img/jn_login.png
copying images... [ 49%] cyverse/../img/jupyter1-1.png
copying images... [ 50%] cyverse/../img/jupyter1-3.png
copying images... [ 52%] cyverse/../img/f1000.png
copying images... [ 53%] docker/../img/auto_build-6.png
copying images... [ 55%] docker/../img/auto_build-2.1.png
copying images... [ 56%] cyverse/../img/jupyter1-8.png
copying images... [ 58%] cyverse/../img/img_building_6.png
copying images... [ 60%] cyverse/../img/img_building_8.png
copying images... [ 61%] docker/../img/private_registry.png
copying images... [ 63%] cyverse/../img/jupyter1-2.png
copying images... [ 64%] docker/../img/dockerhub_autobuilds.png
copying images... [ 66%] breakout/../img/jn_login3.png
copying images... [ 67%] cyverse/../img/jupyter1-4.png
copying images... [ 69%] docker/../img/create_repo.png
copying images... [ 70%] docker/../img/volumes.png
copying images... [ 72%] docker/../img/docker.png
copying images... [ 73%] docker/../img/auto_build-7.png
copying images... [ 75%] docker/../img/auto_build-5.png
copying images... [ 76%] docker/../img/jn_galaxy.png
copying images... [ 78%] breakout/../img/jn_login2.png
copying images... [ 80%] cyverse/../img/jupyter1-5.png
copying images... [ 81%] cyverse/../img/jupyter1-7.png
copying images... [ 83%] cyverse/../img/atmo_cp.png
copying images... [ 84%] docker/../img/dockerhub_buildsettings.png
copying images... [ 86%] cyverse/../img/atmo-6.png
copying images... [ 87%] cyverse/../img/img_building_4.png
copying images... [ 89%] breakout/../img/rstudio_login.png
copying images... [ 90%] cyverse/../img/auto-2.png
copying images... [ 92%] breakout/../img/jn_login3.5.png
copying images... [ 93%] cyverse/../img/atmo_launch1.png
copying images... [ 95%] instructions_reporting/../img/instructors_code.png
copying images... [ 96%] docker/../img/dockerhub_createrepo.png
copying images... [ 98%] getting_started/../img/cyverse_rgb.png
copying images... [100%] singularity/../img/singularity.png

copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/_static' does not exist
done
copying readthedocs static files... done
copying searchtools... done
copying extra files... done
dumping search index in English (code: en) ... done
dumping object inventory... done
build succeeded, 65 warnings.

The HTML pages are in _build/html.

[rtd-command-info] start-time: 2019-07-17T18:00:43.268689Z, end-time: 2019-07-17T18:00:49.625237Z, duration: 6, exit-code: 0
python sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia
Running Sphinx v1.8.5
loading translations [en]... done
making output directory...
loading pickled environment... done
building [mo]: targets for 0 po files that are out of date
building [readthedocssinglehtmllocalmedia]: all documents
updating environment: 55 added, 0 changed, 0 removed
reading sources... [  1%] breakout/biocontainers
reading sources... [  3%] breakout/datascience
reading sources... [  5%] breakout/nvidia-docker
reading sources... [  7%] breakout/workflows
reading sources... [  9%] buildenv/lib/python3.5/site-packages/Babel-2.5.3.dist-info/DESCRIPTION
reading sources... [ 10%] buildenv/lib/python3.5/site-packages/CommonMark-0.5.4.dist-info/DESCRIPTION
reading sources... [ 12%] buildenv/lib/python3.5/site-packages/Jinja2-2.10.dist-info/DESCRIPTION
reading sources... [ 14%] buildenv/lib/python3.5/site-packages/MarkupSafe-1.0.dist-info/DESCRIPTION
reading sources... [ 16%] buildenv/lib/python3.5/site-packages/Pygments-2.2.0.dist-info/DESCRIPTION
reading sources... [ 18%] buildenv/lib/python3.5/site-packages/Sphinx-1.6.6.dist-info/DESCRIPTION
reading sources... [ 20%] buildenv/lib/python3.5/site-packages/alabaster-0.7.10.dist-info/DESCRIPTION
reading sources... [ 21%] buildenv/lib/python3.5/site-packages/certifi-2018.1.18.dist-info/DESCRIPTION
reading sources... [ 23%] buildenv/lib/python3.5/site-packages/chardet-3.0.4.dist-info/DESCRIPTION
reading sources... [ 25%] buildenv/lib/python3.5/site-packages/docutils-0.14.dist-info/DESCRIPTION
reading sources... [ 27%] buildenv/lib/python3.5/site-packages/guzzle_sphinx_theme-0.7.11.dist-info/DESCRIPTION
reading sources... [ 29%] buildenv/lib/python3.5/site-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/README
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages/recommonmark/parser.py:65: UserWarning: Container node skipped: type=document
  warn("Container node skipped: type={0}".format(mdnode.t))
reading sources... [ 30%] buildenv/lib/python3.5/site-packages/idna-2.6.dist-info/DESCRIPTION
reading sources... [ 32%] buildenv/lib/python3.5/site-packages/imagesize-0.7.1.dist-info/DESCRIPTION
reading sources... [ 34%] buildenv/lib/python3.5/site-packages/pip-9.0.1.dist-info/DESCRIPTION
reading sources... [ 36%] buildenv/lib/python3.5/site-packages/pytz-2017.3.dist-info/DESCRIPTION
reading sources... [ 38%] buildenv/lib/python3.5/site-packages/recommonmark-0.4.0.dist-info/DESCRIPTION
reading sources... [ 40%] buildenv/lib/python3.5/site-packages/requests-2.18.4.dist-info/DESCRIPTION
reading sources... [ 41%] buildenv/lib/python3.5/site-packages/setuptools-38.4.0.dist-info/DESCRIPTION
reading sources... [ 43%] buildenv/lib/python3.5/site-packages/six-1.11.0.dist-info/DESCRIPTION
reading sources... [ 45%] buildenv/lib/python3.5/site-packages/snowballstemmer-1.2.1.dist-info/DESCRIPTION
reading sources... [ 47%] buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/base
reading sources... [ 49%] buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/class
reading sources... [ 50%] buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/module
reading sources... [ 52%] buildenv/lib/python3.5/site-packages/sphinx_bootstrap_theme-0.6.4.dist-info/DESCRIPTION
reading sources... [ 54%] buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/DESCRIPTION
reading sources... [ 56%] buildenv/lib/python3.5/site-packages/sphinxcontrib_images-0.7.0.dist-info/DESCRIPTION
reading sources... [ 58%] buildenv/lib/python3.5/site-packages/sphinxcontrib_websupport-1.0.1.dist-info/DESCRIPTION
reading sources... [ 60%] buildenv/lib/python3.5/site-packages/urllib3-1.22.dist-info/DESCRIPTION
reading sources... [ 61%] buildenv/lib/python3.5/site-packages/wheel-0.30.0.dist-info/DESCRIPTION
reading sources... [ 63%] cyverse/boot
reading sources... [ 65%] cyverse/de_docker
reading sources... [ 67%] cyverse/vice_docker
reading sources... [ 69%] docker/dockeradvanced
reading sources... [ 70%] docker/dockerhandson
reading sources... [ 72%] docker/dockerintro
reading sources... [ 74%] getting_started/about_cyverse
reading sources... [ 76%] getting_started/agenda
reading sources... [ 78%] getting_started/installation
reading sources... [ 80%] getting_started/main
reading sources... [ 81%] index
reading sources... [ 83%] instructions_reporting/instructors
reading sources... [ 85%] instructions_reporting/problems
reading sources... [ 87%] singularity/singularityadvanced
reading sources... [ 89%] singularity/singularityintro
reading sources... [ 90%] topics/breakout_session
reading sources... [ 92%] topics/train_docker
reading sources... [ 94%] topics/train_singularity
reading sources... [ 96%] useful_resources/usefulresources_docker
reading sources... [ 98%] useful_resources/usefulresources_other
reading sources... [100%] useful_resources/usefulresources_singularity

/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/breakout/biocontainers.rst:2: WARNING: Title underline too short.

**Biocontainers**
================
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/breakout/datascience.rst:2: WARNING: Duplicate explicit target name: "here".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/requests-2.18.4.dist-info/DESCRIPTION.rst:162: WARNING: Inline emphasis start-string without end-string.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/base.rst:3: WARNING: Error in "currentmodule" directive:
maximum 1 argument(s) allowed, 3 supplied.

.. currentmodule:: {{ module }}
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/class.rst:3: WARNING: Error in "currentmodule" directive:
maximum 1 argument(s) allowed, 3 supplied.

.. currentmodule:: {{ module }}
WARNING: invalid signature for autoclass (u'{{ objname }}')
WARNING: don't know which module to import for autodocumenting u'{{ objname }}' (try placing a "module" or "currentmodule" directive in the document, or giving an explicit module name)
WARNING: invalid signature for automodule (u'{{ fullname }}')
WARNING: don't know which module to import for autodocumenting u'{{ fullname }}' (try placing a "module" or "currentmodule" directive in the document, or giving an explicit module name)
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/DESCRIPTION.rst:: WARNING: image file not readable: buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/screen_mobile.png
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/cyverse/boot.rst:70: WARNING: Content block expected for the "important" directive; none found.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/cyverse/de_docker.rst:4: WARNING: Duplicate explicit target name: "dockerhub".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/cyverse/vice_docker.rst:4: WARNING: Duplicate explicit target name: "here".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockeradvanced.rst:2: WARNING: Duplicate explicit target name: "docker hub".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockeradvanced.rst:441: WARNING: Error in "code-block" directive:
maximum 1 argument(s) allowed, 3 supplied.

.. code-block:: bash
   -v /home/username/your_data_folder:/data:ro
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockeradvanced.rst:527: WARNING: Error in "code-block" directive:
1 argument(s) required, 0 supplied.

.. code-block::

        HOSTNAME=790e13bba28a
        SHLVL=1
        HOME=/root
        PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
        PWD=/
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockerhandson.rst:35: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockerintro.rst:501: WARNING: Duplicate explicit target name: "dockerfile".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockerintro.rst:557: WARNING: Duplicate explicit target name: "build the image".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockerintro.rst:594: WARNING: Duplicate explicit target name: "run your image".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockerintro.rst:473: WARNING: Duplicate target name, cannot be used as a unique reference: "build the image".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockerintro.rst:474: WARNING: Duplicate target name, cannot be used as a unique reference: "run your image".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/getting_started/agenda.rst:2: WARNING: Duplicate explicit target name: "slides".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/getting_started/main.rst:4: WARNING: Title underline too short.

**Workshop Code of Conduct and Other Information**
============================
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityadvanced.rst:7: WARNING: Title underline too short.

5.0 Building your own Containers from scratch
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityadvanced.rst:30: WARNING: Title underline too short.

5.2 Building Singularity containers
==================================
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityadvanced.rst:74: WARNING: Title underline too short.

5.2.1: Exercise (~30 minutes): Create a Singularity file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityadvanced.rst:74: WARNING: Title underline too short.

5.2.1: Exercise (~30 minutes): Create a Singularity file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityadvanced.rst:140: WARNING: Duplicate explicit target name: "user guide".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityadvanced.rst:278: WARNING: Error in "code-block" directive:
maximum 1 argument(s) allowed, 7 supplied.

.. code-block:: bash
  BootStrap: debootstrap
  OSVersion: xenial
  MirrorURL: http://us.archive.ubuntu.com/ubuntu/

  %runscript
      echo "This is what happens when you run the container..."

  %post
      echo "Hello from inside the container"
      sed -i 's/$/ universe/' /etc/apt/sources.list
      apt update
      apt -y --allow-unauthenticated install vim build-essential wget gfortran bison libibverbs-dev libibmad-dev libibumad-dev librdmacm-dev libmlx5-dev libmlx4-dev
      wget http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.1.tar.gz
      tar xvf mvapich2-2.1.tar.gz
      cd mvapich2-2.1
      ./configure --prefix=/usr/local
      make -j4
      make install
      /usr/local/bin/mpicc examples/hellow.c -o /usr/bin/hellow
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityintro.rst:2: WARNING: Duplicate explicit target name: "singularity".
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/Babel-2.5.3.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/CommonMark-0.5.4.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/Jinja2-2.10.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/MarkupSafe-1.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/Pygments-2.2.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/Sphinx-1.6.6.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/alabaster-0.7.10.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/certifi-2018.1.18.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/chardet-3.0.4.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/docutils-0.14.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/guzzle_sphinx_theme-0.7.11.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/README.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/idna-2.6.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/imagesize-0.7.1.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/pip-9.0.1.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/pytz-2017.3.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/recommonmark-0.4.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/requests-2.18.4.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/setuptools-38.4.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/six-1.11.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/snowballstemmer-1.2.1.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/base.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/class.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/module.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx_bootstrap_theme-0.6.4.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinxcontrib_images-0.7.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinxcontrib_websupport-1.0.1.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/urllib3-1.22.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/wheel-0.30.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
done
preparing documents... done
assembling single document... getting_started/main getting_started/installation getting_started/agenda getting_started/about_cyverse topics/train_docker topics/train_singularity topics/breakout_session docker/dockerintro docker/dockeradvanced docker/dockerhandson singularity/singularityintro singularity/singularityadvanced breakout/biocontainers breakout/nvidia-docker breakout/workflows breakout/datascience cyverse/boot cyverse/de_docker cyverse/vice_docker useful_resources/usefulresources_docker useful_resources/usefulresources_singularity useful_resources/usefulresources_other instructions_reporting/instructors instructions_reporting/problems 
writing... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/index.rst:595: WARNING: Could not lex literal_block as "bash". Highlighting skipped.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/index.rst:77: WARNING: Could not lex literal_block as "bash". Highlighting skipped.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/index.rst:112: WARNING: Could not lex literal_block as "bash". Highlighting skipped.
done
writing additional files...
copying images... [  1%] docker/../img/bind_mount.png
copying images... [  3%] cyverse/../img/atmo-8.png
copying images... [  4%] cyverse/../img/jupyter1-6.png
copying images... [  6%] docker/../img/create_repo2.png
copying images... [  7%] docker/../img/docker_image.png
copying images... [  9%] docker/../img/dc-1.png
copying images... [ 10%] breakout/../img/rstudio_login2.png
copying images... [ 12%] cyverse/../img/img_building_5.png
copying images... [ 13%] docker/../img/fastqe.png
copying images... [ 15%] cyverse/../img/auto-3.png
copying images... [ 16%] docker/../img/dockerhub_create.png
copying images... [ 18%] cyverse/../img/auto-4.png
copying images... [ 20%] breakout/../img/snakemake.png
copying images... [ 21%] breakout/../img/jn_login2.png
copying images... [ 23%] instructions_reporting/../img/static_site_docker.png
copying images... [ 24%] cyverse/../img/f1000.png
copying images... [ 26%] cyverse/../img/atmo-9.png
copying images... [ 27%] cyverse/../img/img_building_9.png
copying images... [ 29%] docker/../img/portainer_demo.png
copying images... [ 30%] cyverse/../img/img_building_3.png
copying images... [ 32%] cyverse/../img/img_building_1.png
copying images... [ 33%] breakout/../img/rstudio_ss.png
copying images... [ 35%] docker/../img/dockerhub_autobuild.png
copying images... [ 36%] cyverse/../img/auto-1.png
copying images... [ 38%] cyverse/../img/atmo_launch0.png
copying images... [ 40%] docker/../img/volumes.png
copying images... [ 41%] docker/../img/jn_login.png
copying images... [ 43%] cyverse/../img/atmo-1.1.png
copying images... [ 44%] cyverse/../img/cyverse_rgb.png
copying images... [ 46%] breakout/../img/jn_login3.5.png
copying images... [ 47%] breakout/../img/jn_login.png
copying images... [ 49%] cyverse/../img/jupyter1-1.png
copying images... [ 50%] docker/../img/dockerhub_createrepo.png
copying images... [ 52%] cyverse/../img/atmo_launch.png
copying images... [ 53%] docker/../img/pwd.png
copying images... [ 55%] docker/../img/auto_build-6.png
copying images... [ 56%] docker/../img/auto_build-7.png
copying images... [ 58%] cyverse/../img/jupyter1-8.png
copying images... [ 60%] cyverse/../img/img_building_6.png
copying images... [ 61%] cyverse/../img/img_building_8.png
copying images... [ 63%] docker/../img/private_registry.png
copying images... [ 64%] cyverse/../img/jupyter1-2.png
copying images... [ 66%] docker/../img/dockerhub_autobuilds.png
copying images... [ 67%] breakout/../img/jn_login3.png
copying images... [ 69%] docker/../img/create_repo.png
copying images... [ 70%] instructions_reporting/../img/instructors_code.png
copying images... [ 72%] docker/../img/docker.png
copying images... [ 73%] cyverse/../img/jupyter1-5.png
copying images... [ 75%] docker/../img/jn_galaxy.png
copying images... [ 76%] cyverse/../img/jupyter1-3.png
copying images... [ 78%] cyverse/../img/jupyter1-4.png
copying images... [ 80%] docker/../img/auto_build-5.png
copying images... [ 81%] cyverse/../img/jupyter1-7.png
copying images... [ 83%] docker/../img/dockerhub_buildsettings.png
copying images... [ 84%] cyverse/../img/atmo_cp.png
copying images... [ 86%] docker/../img/auto_build-2.1.png
copying images... [ 87%] cyverse/../img/atmo-6.png
copying images... [ 89%] cyverse/../img/img_building_4.png
copying images... [ 90%] breakout/../img/rstudio_login.png
copying images... [ 92%] cyverse/../img/auto-2.png
copying images... [ 93%] ./img/cc-main.png
copying images... [ 95%] cyverse/../img/atmo_launch1.png
copying images... [ 96%] cyverse/../img/jupyter1-9.png
copying images... [ 98%] getting_started/../img/cyverse_rgb.png
copying images... [100%] singularity/../img/singularity.png

copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/_static' does not exist
done
copying readthedocs static files... done
copying extra files... done
dumping object inventory... done
build succeeded, 65 warnings.

The HTML page is in _build/localmedia.

[rtd-command-info] start-time: 2019-07-17T18:00:49.831988Z, end-time: 2019-07-17T18:00:55.734794Z, duration: 5, exit-code: 0
python sphinx-build -b latex -D language=en -d _build/doctrees . _build/latex
Running Sphinx v1.8.5
loading translations [en]... done
making output directory...
loading pickled environment... done
building [mo]: targets for 0 po files that are out of date
building [latex]: all documents
updating environment: 55 added, 0 changed, 0 removed
reading sources... [  1%] breakout/biocontainers
reading sources... [  3%] breakout/datascience
reading sources... [  5%] breakout/nvidia-docker
reading sources... [  7%] breakout/workflows
reading sources... [  9%] buildenv/lib/python3.5/site-packages/Babel-2.5.3.dist-info/DESCRIPTION
reading sources... [ 10%] buildenv/lib/python3.5/site-packages/CommonMark-0.5.4.dist-info/DESCRIPTION
reading sources... [ 12%] buildenv/lib/python3.5/site-packages/Jinja2-2.10.dist-info/DESCRIPTION
reading sources... [ 14%] buildenv/lib/python3.5/site-packages/MarkupSafe-1.0.dist-info/DESCRIPTION
reading sources... [ 16%] buildenv/lib/python3.5/site-packages/Pygments-2.2.0.dist-info/DESCRIPTION
reading sources... [ 18%] buildenv/lib/python3.5/site-packages/Sphinx-1.6.6.dist-info/DESCRIPTION
reading sources... [ 20%] buildenv/lib/python3.5/site-packages/alabaster-0.7.10.dist-info/DESCRIPTION
reading sources... [ 21%] buildenv/lib/python3.5/site-packages/certifi-2018.1.18.dist-info/DESCRIPTION
reading sources... [ 23%] buildenv/lib/python3.5/site-packages/chardet-3.0.4.dist-info/DESCRIPTION
reading sources... [ 25%] buildenv/lib/python3.5/site-packages/docutils-0.14.dist-info/DESCRIPTION
reading sources... [ 27%] buildenv/lib/python3.5/site-packages/guzzle_sphinx_theme-0.7.11.dist-info/DESCRIPTION
reading sources... [ 29%] buildenv/lib/python3.5/site-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/README
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages/recommonmark/parser.py:65: UserWarning: Container node skipped: type=document
  warn("Container node skipped: type={0}".format(mdnode.t))
reading sources... [ 30%] buildenv/lib/python3.5/site-packages/idna-2.6.dist-info/DESCRIPTION
reading sources... [ 32%] buildenv/lib/python3.5/site-packages/imagesize-0.7.1.dist-info/DESCRIPTION
reading sources... [ 34%] buildenv/lib/python3.5/site-packages/pip-9.0.1.dist-info/DESCRIPTION
reading sources... [ 36%] buildenv/lib/python3.5/site-packages/pytz-2017.3.dist-info/DESCRIPTION
reading sources... [ 38%] buildenv/lib/python3.5/site-packages/recommonmark-0.4.0.dist-info/DESCRIPTION
reading sources... [ 40%] buildenv/lib/python3.5/site-packages/requests-2.18.4.dist-info/DESCRIPTION
reading sources... [ 41%] buildenv/lib/python3.5/site-packages/setuptools-38.4.0.dist-info/DESCRIPTION
reading sources... [ 43%] buildenv/lib/python3.5/site-packages/six-1.11.0.dist-info/DESCRIPTION
reading sources... [ 45%] buildenv/lib/python3.5/site-packages/snowballstemmer-1.2.1.dist-info/DESCRIPTION
reading sources... [ 47%] buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/base
reading sources... [ 49%] buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/class
reading sources... [ 50%] buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/module
reading sources... [ 52%] buildenv/lib/python3.5/site-packages/sphinx_bootstrap_theme-0.6.4.dist-info/DESCRIPTION
reading sources... [ 54%] buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/DESCRIPTION
reading sources... [ 56%] buildenv/lib/python3.5/site-packages/sphinxcontrib_images-0.7.0.dist-info/DESCRIPTION
reading sources... [ 58%] buildenv/lib/python3.5/site-packages/sphinxcontrib_websupport-1.0.1.dist-info/DESCRIPTION
reading sources... [ 60%] buildenv/lib/python3.5/site-packages/urllib3-1.22.dist-info/DESCRIPTION
reading sources... [ 61%] buildenv/lib/python3.5/site-packages/wheel-0.30.0.dist-info/DESCRIPTION
reading sources... [ 63%] cyverse/boot
reading sources... [ 65%] cyverse/de_docker
reading sources... [ 67%] cyverse/vice_docker
reading sources... [ 69%] docker/dockeradvanced
reading sources... [ 70%] docker/dockerhandson
reading sources... [ 72%] docker/dockerintro
reading sources... [ 74%] getting_started/about_cyverse
reading sources... [ 76%] getting_started/agenda
reading sources... [ 78%] getting_started/installation
reading sources... [ 80%] getting_started/main
reading sources... [ 81%] index
reading sources... [ 83%] instructions_reporting/instructors
reading sources... [ 85%] instructions_reporting/problems
reading sources... [ 87%] singularity/singularityadvanced
reading sources... [ 89%] singularity/singularityintro
reading sources... [ 90%] topics/breakout_session
reading sources... [ 92%] topics/train_docker
reading sources... [ 94%] topics/train_singularity
reading sources... [ 96%] useful_resources/usefulresources_docker
reading sources... [ 98%] useful_resources/usefulresources_other
reading sources... [100%] useful_resources/usefulresources_singularity

/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/breakout/biocontainers.rst:2: WARNING: Title underline too short.

**Biocontainers**
================
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/breakout/datascience.rst:2: WARNING: Duplicate explicit target name: "here".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/requests-2.18.4.dist-info/DESCRIPTION.rst:162: WARNING: Inline emphasis start-string without end-string.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/base.rst:3: WARNING: Error in "currentmodule" directive:
maximum 1 argument(s) allowed, 3 supplied.

.. currentmodule:: {{ module }}
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/class.rst:3: WARNING: Error in "currentmodule" directive:
maximum 1 argument(s) allowed, 3 supplied.

.. currentmodule:: {{ module }}
WARNING: invalid signature for autoclass (u'{{ objname }}')
WARNING: don't know which module to import for autodocumenting u'{{ objname }}' (try placing a "module" or "currentmodule" directive in the document, or giving an explicit module name)
WARNING: invalid signature for automodule (u'{{ fullname }}')
WARNING: don't know which module to import for autodocumenting u'{{ fullname }}' (try placing a "module" or "currentmodule" directive in the document, or giving an explicit module name)
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/DESCRIPTION.rst:: WARNING: image file not readable: buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/screen_mobile.png
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/cyverse/boot.rst:70: WARNING: Content block expected for the "important" directive; none found.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/cyverse/de_docker.rst:4: WARNING: Duplicate explicit target name: "dockerhub".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/cyverse/vice_docker.rst:4: WARNING: Duplicate explicit target name: "here".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockeradvanced.rst:2: WARNING: Duplicate explicit target name: "docker hub".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockeradvanced.rst:441: WARNING: Error in "code-block" directive:
maximum 1 argument(s) allowed, 3 supplied.

.. code-block:: bash
   -v /home/username/your_data_folder:/data:ro
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockeradvanced.rst:527: WARNING: Error in "code-block" directive:
1 argument(s) required, 0 supplied.

.. code-block::

        HOSTNAME=790e13bba28a
        SHLVL=1
        HOME=/root
        PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
        PWD=/
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockerhandson.rst:35: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockerintro.rst:501: WARNING: Duplicate explicit target name: "dockerfile".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockerintro.rst:557: WARNING: Duplicate explicit target name: "build the image".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockerintro.rst:594: WARNING: Duplicate explicit target name: "run your image".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockerintro.rst:473: WARNING: Duplicate target name, cannot be used as a unique reference: "build the image".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockerintro.rst:474: WARNING: Duplicate target name, cannot be used as a unique reference: "run your image".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/getting_started/agenda.rst:2: WARNING: Duplicate explicit target name: "slides".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/getting_started/main.rst:4: WARNING: Title underline too short.

**Workshop Code of Conduct and Other Information**
============================
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityadvanced.rst:7: WARNING: Title underline too short.

5.0 Building your own Containers from scratch
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityadvanced.rst:30: WARNING: Title underline too short.

5.2 Building Singularity containers
==================================
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityadvanced.rst:74: WARNING: Title underline too short.

5.2.1: Exercise (~30 minutes): Create a Singularity file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityadvanced.rst:74: WARNING: Title underline too short.

5.2.1: Exercise (~30 minutes): Create a Singularity file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityadvanced.rst:140: WARNING: Duplicate explicit target name: "user guide".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityadvanced.rst:278: WARNING: Error in "code-block" directive:
maximum 1 argument(s) allowed, 7 supplied.

.. code-block:: bash
  BootStrap: debootstrap
  OSVersion: xenial
  MirrorURL: http://us.archive.ubuntu.com/ubuntu/

  %runscript
      echo "This is what happens when you run the container..."

  %post
      echo "Hello from inside the container"
      sed -i 's/$/ universe/' /etc/apt/sources.list
      apt update
      apt -y --allow-unauthenticated install vim build-essential wget gfortran bison libibverbs-dev libibmad-dev libibumad-dev librdmacm-dev libmlx5-dev libmlx4-dev
      wget http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.1.tar.gz
      tar xvf mvapich2-2.1.tar.gz
      cd mvapich2-2.1
      ./configure --prefix=/usr/local
      make -j4
      make install
      /usr/local/bin/mpicc examples/hellow.c -o /usr/bin/hellow
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityintro.rst:2: WARNING: Duplicate explicit target name: "singularity".
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/Babel-2.5.3.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/CommonMark-0.5.4.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/Jinja2-2.10.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/MarkupSafe-1.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/Pygments-2.2.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/Sphinx-1.6.6.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/alabaster-0.7.10.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/certifi-2018.1.18.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/chardet-3.0.4.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/docutils-0.14.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/guzzle_sphinx_theme-0.7.11.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/README.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/idna-2.6.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/imagesize-0.7.1.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/pip-9.0.1.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/pytz-2017.3.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/recommonmark-0.4.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/requests-2.18.4.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/setuptools-38.4.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/six-1.11.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/snowballstemmer-1.2.1.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/base.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/class.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/module.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx_bootstrap_theme-0.6.4.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinxcontrib_images-0.7.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinxcontrib_websupport-1.0.1.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/urllib3-1.22.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/wheel-0.30.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
done
processing CyVerseDocumentation.tex...index getting_started/main getting_started/installation getting_started/agenda getting_started/about_cyverse topics/train_docker topics/train_singularity topics/breakout_session docker/dockerintro docker/dockeradvanced docker/dockerhandson singularity/singularityintro singularity/singularityadvanced breakout/biocontainers breakout/nvidia-docker breakout/workflows breakout/datascience cyverse/boot cyverse/de_docker cyverse/vice_docker useful_resources/usefulresources_docker useful_resources/usefulresources_singularity useful_resources/usefulresources_other instructions_reporting/instructors instructions_reporting/problems 
resolving references...
writing... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockeradvanced.rst:595: WARNING: Could not lex literal_block as "bash". Highlighting skipped.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityintro.rst:77: WARNING: Could not lex literal_block as "bash". Highlighting skipped.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityintro.rst:112: WARNING: Could not lex literal_block as "bash". Highlighting skipped.
done
copying images... [  1%] docker/../img/bind_mount.png
copying images... [  2%] cyverse/../img/atmo-8.png
copying images... [  4%] https://cloud.githubusercontent.com/assets/3028125/12213714/5b208976-b632-11e5-8406-38d379ec46aa.png
copying images... [  5%] cyverse/../img/jupyter1-6.png
copying images... [  7%] docker/../img/create_repo2.png
copying images... [  8%] docker/../img/docker_image.png
copying images... [ 10%] docker/../img/dc-1.png
copying images... [ 11%] breakout/../img/rstudio_login2.png
copying images... [ 13%] cyverse/../img/img_building_5.png
copying images... [ 14%] docker/../img/fastqe.png
copying images... [ 16%] cyverse/../img/auto-3.png
copying images... [ 17%] docker/../img/dockerhub_create.png
copying images... [ 19%] cyverse/../img/auto-4.png
copying images... [ 20%] breakout/../img/snakemake.png
copying images... [ 22%] breakout/../img/jn_login2.png
copying images... [ 23%] instructions_reporting/../img/static_site_docker.png
copying images... [ 25%] cyverse/../img/f1000.png
copying images... [ 26%] cyverse/../img/atmo-9.png
copying images... [ 28%] cyverse/../img/img_building_9.png
copying images... [ 29%] docker/../img/portainer_demo.png
copying images... [ 31%] cyverse/../img/img_building_3.png
copying images... [ 32%] cyverse/../img/img_building_1.png
copying images... [ 34%] breakout/../img/rstudio_ss.png
copying images... [ 35%] docker/../img/dockerhub_autobuild.png
copying images... [ 37%] cyverse/../img/auto-1.png
copying images... [ 38%] cyverse/../img/atmo_launch0.png
copying images... [ 40%] docker/../img/volumes.png
copying images... [ 41%] docker/../img/jn_login.png
copying images... [ 43%] cyverse/../img/atmo-1.1.png
copying images... [ 44%] cyverse/../img/cyverse_rgb.png
copying images... [ 46%] breakout/../img/jn_login3.5.png
copying images... [ 47%] breakout/../img/jn_login.png
copying images... [ 49%] cyverse/../img/jupyter1-1.png
copying images... [ 50%] docker/../img/dockerhub_createrepo.png
copying images... [ 52%] cyverse/../img/atmo_launch.png
copying images... [ 53%] docker/../img/pwd.png
copying images... [ 55%] docker/../img/auto_build-6.png
copying images... [ 56%] docker/../img/auto_build-7.png
copying images... [ 58%] cyverse/../img/jupyter1-8.png
copying images... [ 59%] cyverse/../img/img_building_6.png
copying images... [ 61%] cyverse/../img/img_building_8.png
copying images... [ 62%] docker/../img/private_registry.png
copying images... [ 64%] http://singularity.lbl.gov/assets/img/diagram/singularity-2.4-flow.png
copying images... [ 65%] cyverse/../img/jupyter1-2.png
copying images... [ 67%] docker/../img/dockerhub_autobuilds.png
copying images... [ 68%] breakout/../img/jn_login3.png
copying images... [ 70%] docker/../img/create_repo.png
copying images... [ 71%] instructions_reporting/../img/instructors_code.png
copying images... [ 73%] docker/../img/docker.png
copying images... [ 74%] cyverse/../img/jupyter1-5.png
copying images... [ 76%] docker/../img/jn_galaxy.png
copying images... [ 77%] cyverse/../img/jupyter1-3.png
copying images... [ 79%] cyverse/../img/jupyter1-4.png
copying images... [ 80%] docker/../img/auto_build-5.png
copying images... [ 82%] cyverse/../img/jupyter1-7.png
copying images... [ 83%] docker/../img/dockerhub_buildsettings.png
copying images... [ 85%] cyverse/../img/atmo_cp.png
copying images... [ 86%] docker/../img/auto_build-2.1.png
copying images... [ 88%] cyverse/../img/atmo-6.png
copying images... [ 89%] cyverse/../img/img_building_4.png
copying images... [ 91%] breakout/../img/rstudio_login.png
copying images... [ 92%] cyverse/../img/auto-2.png
copying images... [ 94%] ./img/cc-main.png
copying images... [ 95%] cyverse/../img/atmo_launch1.png
copying images... [ 97%] cyverse/../img/jupyter1-9.png
copying images... [ 98%] getting_started/../img/cyverse_rgb.png
copying images... [100%] singularity/../img/singularity.png

copying TeX support files...
done
build succeeded, 64 warnings.

The LaTeX files are in _build/latex.
Run 'make' in that directory to run these through (pdf)latex
(use `make latexpdf' here to do that automatically).

[rtd-command-info] start-time: 2019-07-17T18:01:24.361832Z, end-time: 2019-07-17T18:01:24.742572Z, duration: 0, exit-code: 0
cat latexmkrc
$latex = 'latex ' . $ENV{'LATEXOPTS'} . ' %O %S';
$pdflatex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' %O %S';
$lualatex = 'lualatex ' . $ENV{'LATEXOPTS'} . ' %O %S';
$xelatex = 'xelatex --no-pdf ' . $ENV{'LATEXOPTS'} . ' %O %S';
$makeindex = 'makeindex -s python.ist %O -o %D %S';
add_cus_dep( "glo", "gls", 0, "makeglo" );
sub makeglo {
 return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" );
}

[rtd-command-info] start-time: 2019-07-17T18:01:24.824259Z, end-time: 2019-07-17T18:02:13.491005Z, duration: 48, exit-code: 0
latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=cyverse-container-camp-workshop-2019 -interaction=nonstopmode
Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 1, <GEN1> chunk 1.
Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 2, <GEN1> chunk 1.
Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 3, <GEN1> chunk 1.
Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 4, <GEN1> chunk 1.
Subroutine makeglo redefined at (eval 11) line 7, <GEN2> chunk 1.
Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 1, <GEN2> chunk 1.
Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 2, <GEN2> chunk 1.
Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 3, <GEN2> chunk 1.
Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 4, <GEN2> chunk 1.
Latexmk: This is Latexmk, John Collins, 1 January 2015, version: 4.41.
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/bin/latexmk line 7482.
Rule 'pdflatex': Rules & subrules not known to be previously run:
   pdflatex
Rule 'pdflatex': The following rules & subrules became out-of-date:
      'pdflatex'
------------
Run number 1 of rule 'pdflatex'
------------
------------
Running 'pdflatex   -interaction=nonstopmode -recorder --jobname="cyverse-container-camp-workshop-2019"  "CyVerseDocumentation.tex"'
------------
Latexmk: applying rule 'pdflatex'...
This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./CyVerseDocumentation.tex
LaTeX2e <2017-04-15>
Babel <3.18> and hyphenation patterns for 84 language(s) loaded.
(./sphinxmanual.cls
Document Class: sphinxmanual 2018/12/22 v1.8.3 Document class (Sphinx manual)
(/usr/share/texlive/texmf-dist/tex/latex/base/report.cls
Document Class: report 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)))
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)))
(/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)<<t1.cmap>>)
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty
For additional information on amsmath, use the `?' option.
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty))
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty)
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty))
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty))
(/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty
(/usr/share/texlive/texmf-dist/tex/generic/babel/switch.def)
(/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf
(/usr/share/texlive/texmf-dist/tex/generic/babel/babel.def
(/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def))))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/fncychap/fncychap.sty) (./sphinx.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))
(/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu)))
(/usr/share/texlive/texmf-dist/tex/latex/titlesec/titlesec.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tabulary/tabulary.sty
(/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty))
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/varwidth/varwidth.sty)
(./sphinxmulticell.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty)
(/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty
Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix 
<2008/02/07> (tvz)) (./footnotehyper-sphinx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/float/float.sty)
(/usr/share/texlive/texmf-dist/tex/latex/wrapfig/wrapfig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty)
(/usr/share/texlive/texmf-dist/tex/latex/capt-of/capt-of.sty)
(/usr/share/texlive/texmf-dist/tex/latex/needspace/needspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/carlisle/remreset.sty)
(./sphinxhighlight.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty)
Writing index file cyverse-container-camp-workshop-2019.idx
(./cyverse-container-camp-workshop-2019.aux)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)<<ot1.cmap>><<oml.cmap
>><<oms.cmap>><<omx.cmap>>
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd)
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}] [2] [1] [2]
Overfull \hbox (132.49107pt too wide) in paragraph at lines 83--84
[][] 
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [1 <./cc-main.png> <
./cyverse_rgb1.png>] [2]
Chapter 1.
[3] [4]
Chapter 2.
[5]
Underfull \hbox (badness 5189) in paragraph at lines 2--288
[][][]\T1/ptm/m/n/10 Download Cy-Verse Cy-ber-
[6]
Chapter 3.

Underfull \hbox (badness 5802) in paragraph at lines 332--333
[]|\T1/ptm/m/n/10 General in-tro-duc-tion to

Underfull \hbox (badness 6675) in paragraph at lines 339--340
\T1/ptm/m/n/10 tainer tech-nol-ogy land-

Underfull \hbox (badness 10000) in paragraph at lines 353--354
[]|\T1/ptm/m/n/10 Introduction to Docker

Underfull \hbox (badness 6412) in paragraph at lines 360--361
[]|\T1/ptm/m/n/10 Lunch break (on your

Underfull \hbox (badness 10000) in paragraph at lines 379--380
[]|\T1/ptm/m/n/10 Docker hands-on ex-er-

Underfull \hbox (badness 10000) in paragraph at lines 2--383
[]|[][]\T1/ptm/m/n/10 Docker hands-on ex-er-

Underfull \hbox (badness 6961) in paragraph at lines 400--401
[]|\T1/ptm/m/n/10 Review Day 1 (Ques-

Underfull \hbox (badness 10000) in paragraph at lines 2--421
[][][]\T1/ptm/m/n/10 Non-interactive

Underfull \hbox (badness 10000) in paragraph at lines 1--441
[][][]$\T1/ptm/m/n/10 https : / / mirrorlab .

Underfull \hbox (badness 10000) in paragraph at lines 1--444
[][][]$\T1/ptm/m/n/10 https : / / it . arizona .

Underfull \hbox (badness 10000) in paragraph at lines 1--444
\T1/ptm/m/n/10 edu / service /

Overfull \hbox (38.81021pt too wide) in paragraph at lines 1--444
\T1/ptm/m/n/10 high-[]performance-[]computing$[][] 

Underfull \hbox (badness 5832) in paragraph at lines 462--463
[]|\T1/ptm/m/n/10 500k con-tain-ers a day

Underfull \hbox (badness 10000) in paragraph at lines 462--463
\T1/ptm/m/n/10 - Re-mote Pre-sen-ta-tion

Underfull \hbox (badness 10000) in paragraph at lines 2--480
[][][]\T1/ptm/m/n/10 Singularity in-tro-

Underfull \hbox (badness 10000) in paragraph at lines 2--483
[][][]\T1/ptm/m/n/10 Singularity in-tro-

Underfull \hbox (badness 10000) in paragraph at lines 494--495
[]|\T1/ptm/m/n/10 Advanced Sin-gu-lar-ity
[7]
Overfull \vbox (237.30956pt too high) has occurred while \output is active
[8]
Chapter 4.
[9] [10]
Chapter 5.
[11] [12]
Chapter 6.
[13] [14]
Chapter 7.
[15] [16]
Chapter 8.
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [17 <./docker.png>]
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [18] [19] [20]
[21] [22] [23]
Underfull \hbox (badness 10000) in paragraph at lines 1041--1043
\T1/ptm/b/n/10 Note:  \T1/ptm/m/n/10 When you run the \T1/pcr/m/n/10 docker bui
ld \T1/ptm/m/n/10 com-mand given be-low, make sure to re-place
[24]
Overfull \vbox (11.24115pt too high) detected at line 1126
[25]

LaTeX Warning: Hyper reference `docker/dockerintro:create-a-python-file-contain
ing-a-function' on page 26 undefined on input line 1134.

[26] [27] [28] [29] [30 <./portainer_demo.png>] [31 <./pwd.png>] [32]
Chapter 9.
[33] [34] [35 <./docker_image.png>] [36 <./private_registry.png>] [37]
Overfull \hbox (132.49107pt too wide) in paragraph at lines 1699--1700
[][] 

Overfull \hbox (132.49107pt too wide) in paragraph at lines 1710--1711
[][] 
[38 <./dockerhub_create.png>]
Overfull \hbox (132.49107pt too wide) in paragraph at lines 1724--1725
[][] 
[39 <./dockerhub_createrepo.png>]
Overfull \hbox (132.49107pt too wide) in paragraph at lines 1728--1729
[][] 
[40 <./dockerhub_buildsettings.png>] [41 <./dockerhub_autobuild.png>] [42 <./cr
eate_repo.png> <./create_repo2.png>]
Overfull \hbox (132.49107pt too wide) in paragraph at lines 1832--1833
[][] 
[43]
Overfull \vbox (90.47859pt too high) has occurred while \output is active
[44 <./dockerhub_autobuilds.png>] [45 <./auto_build-2.1.png>] [46 <./auto_build
-5.png> <./auto_build-6.png>] [47 <./auto_build-7.png>] [48 <./volumes.png>]
Underfull \hbox (badness 10000) in paragraph at lines 2050--2052
\T1/ptm/b/n/10 Note:  \T1/ptm/m/n/10 File lo-ca-tion on Mac OS X is a bit dif-f
er-ent: [][]$https : / / timonweb . com / posts /
[49] [50] [51 <./bind_mount.png>] [52] [53] [54] [55 <./dc-1.png>] [56]
Chapter 10.

Overfull \hbox (57.21031pt too wide) in paragraph at lines 2429--2430
[][] 
[57 <./fastqe.png>] [58] [59]
Overfull \vbox (9.74088pt too high) detected at line 2581
[60]
Overfull \hbox (57.20003pt too wide) in paragraph at lines 2593--2594
| []|  

Underfull \hbox (badness 10000) in paragraph at lines 2595--2596
[]\T1/ptm/m/n/10 You should be greeted by your own con-tainer-ised Jupyter ser-
vice! Now open \T1/pcr/m/n/10 galaxy/

Overfull \hbox (57.22421pt too wide) in paragraph at lines 2597--2598
| []|  
[61 <./jn_login1.png>] [62 <./jn_galaxy.png>]
Chapter 11.
[63 <./singularity.png>]
Overfull \hbox (132.49107pt too wide) in paragraph at lines 2647--2648
[][] 
[64 <./singularity-2.4-flow.png>]
Overfull \hbox (70.24437pt too wide) in paragraph at lines 2720--2720
[][]\T1/pcr/m/n/9 [[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=
[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]
=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][
]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[]
[]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[
][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=
[][]=[][]=[][]=[][]=[][]][][] 
[65]
Underfull \vbox (badness 1874) detected at line 2816
[66] [67]
Overfull \hbox (70.24437pt too wide) in paragraph at lines 2864--2864
[][]\T1/pcr/m/n/9 [[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=
[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]
=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][
]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[]
[]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[
][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=
[][]=[][]=[][]=[][]=[][]][][] 

Overfull \hbox (70.24437pt too wide) in paragraph at lines 2872--2872
[][]\T1/pcr/m/n/9 [[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=
[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]
=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][
]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[]
[]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[
][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=
[][]=[][]=[][]=[][]=[][]][][] 
[68]
Overfull \hbox (86.44435pt too wide) in paragraph at lines 2916--2916
[][]\T1/pcr/m/n/9 [[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=
[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]
=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][
]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[]
[]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[
][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=
[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]][][] 
[69] [70] [71] [72]
Chapter 12.
[73] [74] [75] [76]
Chapter 13.
[77]
Overfull \vbox (6.28346pt too high) detected at line 3399
[78] [79] [80] [81] [82]
Chapter 14.

Underfull \hbox (badness 10000) in paragraph at lines 3508--3509
\T1/ptm/m/n/10 Biocontainers for con-tainer camp by Amanda Cook-sey - [][]$http
s : / / de . cyverse . org / dl / d /
[83] [84]
Chapter 15.

Overfull \hbox (132.49107pt too wide) in paragraph at lines 3521--3522
[] 
[85] [86 <./dff16156a2fac35ba7650c7bae20c561e0b8d2e8.png>] [87] [88]
Chapter 16.

Overfull \hbox (57.21031pt too wide) in paragraph at lines 3572--3573
[] 
[89 <./snakemake.png>] [90]
Chapter 17.
[91]

! Package inputenc Error: Unicode char   (U+200A)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.3655 ...your version of Linux/Windows/OSX/OS9 
                                                  — well this is where D...


! Package inputenc Error: Unicode char   (U+200A)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.3655 ...ersion of Linux/Windows/OSX/OS9 — 
                                                  well this is where Docker ...


Overfull \hbox (57.21031pt too wide) in paragraph at lines 3668--3669
[][] 

Overfull \hbox (57.21031pt too wide) in paragraph at lines 3672--3673
[][] 
[92 <./jn_login.png>]
Overfull \hbox (57.21031pt too wide) in paragraph at lines 3676--3677
[][] 

Overfull \hbox (57.21031pt too wide) in paragraph at lines 3678--3679
[][] 
[93 <./jn_login2.png> <./jn_login3.png>]

! Package inputenc Error: Unicode char   (U+200A)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.3698 ...r compose file. And there you have it 
                                                  — a quick and easy way...


! Package inputenc Error: Unicode char   (U+200A)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.3698 ...ose file. And there you have it — 
                                                  a quick and easy way to st...


Overfull \hbox (57.21031pt too wide) in paragraph at lines 3705--3706
[][] 
[94 <./jn_login3.5.png>]
Overfull \hbox (57.21031pt too wide) in paragraph at lines 3713--3714
[][] 
[95 <./rstudio_ss.png> <./rstudio_login2.png>]
Overfull \hbox (57.21031pt too wide) in paragraph at lines 3719--3720
[][] 

! Package inputenc Error: Unicode char   (U+200A)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.3755 ...sphinxupquote{requirements.txt}} file 
                                                  — Contains python modu...


! Package inputenc Error: Unicode char   (U+200A)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.3755 ...upquote{requirements.txt}} file — 
                                                  Contains python modules an...


! Package inputenc Error: Unicode char   (U+200A)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.3770 ...inxupquote{app.py}} inside the folder 
                                                  — \sphinxcode{\sphinxupq...

[96 <./rstudio_login.png>] [97] [98] [99 <./cyverse_rgb.png>] [100]
Chapter 18.

Overfull \hbox (57.2353pt too wide) in paragraph at lines 3970--3971
[][] 
[101]
Overfull \hbox (57.2342pt too wide) in paragraph at lines 3995--3996
[][] 
[102 <./atmo-1.1.png>]
Overfull \hbox (57.21959pt too wide) in paragraph at lines 4014--4015
[][] 
[103 <./atmo_cp.png>]
Overfull \hbox (57.20882pt too wide) in paragraph at lines 4021--4022
[][] 
[104 <./atmo_launch0.png> <./atmo_launch1.png>]
Overfull \hbox (57.22607pt too wide) in paragraph at lines 4031--4032
[][] 

Overfull \hbox (57.23694pt too wide) in paragraph at lines 4041--4042
[][] 
[105 <./atmo_launch.png>]
Overfull \hbox (57.22354pt too wide) in paragraph at lines 4061--4062
[][] 
[106 <./atmo-6.png>]
Overfull \hbox (57.21503pt too wide) in paragraph at lines 4070--4071
[][] 
[107 <./atmo-8.png>] [108 <./atmo-9.png>]
Chapter 19.

Overfull \hbox (57.21031pt too wide) in paragraph at lines 4085--4086
[][] 

LaTeX Warning: Hyper reference `cyverse/de_docker:build-and-test-your-docker-im
ages' on page 109 undefined on input line 4094.


LaTeX Warning: Hyper reference `cyverse/de_docker:push-your-docker-image-to-doc
kerhub' on page 109 undefined on input line 4097.


LaTeX Warning: Hyper reference `cyverse/de_docker:add-docker-images-as-tool-in-
de' on page 109 undefined on input line 4100.

[109 <./f1000.png>]

LaTeX Warning: Hyper reference `cyverse/de_docker:create-an-app-ui-for-the-tool
-in-de' on page 110 undefined on input line 4103.


LaTeX Warning: Hyper reference `cyverse/de_docker:test-the-app-using-appropriat
e-test-data-in-de' on page 110 undefined on input line 4106.


Overfull \hbox (57.21031pt too wide) in paragraph at lines 4150--4151
[][] 

Overfull \hbox (57.21031pt too wide) in paragraph at lines 4154--4155
[][] 
[110 <./auto-1.png>]
Overfull \hbox (57.21031pt too wide) in paragraph at lines 4158--4159
[][] 
[111 <./auto-2.png>]
Overfull \hbox (57.21031pt too wide) in paragraph at lines 4162--4163
[][] 
[112 <./auto-3.png>]
Overfull \hbox (57.21031pt too wide) in paragraph at lines 4225--4226
[][] 
[113 <./auto-4.png>]
Overfull \hbox (57.21031pt too wide) in paragraph at lines 4250--4251
[][] 
[114 <./img_building_1.png>]
Overfull \hbox (57.21031pt too wide) in paragraph at lines 4258--4259
[][] 
[115 <./img_building_4.png> <./img_building_3.png>]
Overfull \hbox (57.21031pt too wide) in paragraph at lines 4277--4278
[][] 

Overfull \hbox (57.21031pt too wide) in paragraph at lines 4288--4289
[][] 
[116 <./img_building_9.png> <./img_building_5.png>]
Overfull \hbox (57.21031pt too wide) in paragraph at lines 4299--4300
[][] 
[117 <./img_building_6.png> <./img_building_8.png>] [118]
Chapter 20.

Overfull \hbox (57.20361pt too wide) in paragraph at lines 4329--4330
[][] 
[119]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 4336--4337
[][] 
[120 <./jupyter1-1.png>]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 4338--4339
[][] 
[121 <./jupyter1-2.png> <./jupyter1-3.png>]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 4349--4350
[][] 

Overfull \hbox (57.20361pt too wide) in paragraph at lines 4353--4354
[][] 
[122 <./jupyter1-9.png>]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 4372--4373
[][] 
[123 <./jupyter1-4.png>]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 4383--4384
[][] 
[124 <./jupyter1-5.png>]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 4390--4391
[][] 
[125 <./jupyter1-6.png>]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 4392--4393
[][] 
[126 <./jupyter1-7.png> <./jupyter1-8.png>] [127] [128]
Chapter 21.
[129] [130]
Chapter 22.
[131] [132]
Chapter 23.
[133] [134]
Chapter 24.
[135]
Overfull \hbox (94.8507pt too wide) in paragraph at lines 4604--4605
[][] 
[136]
Overfull \hbox (94.8507pt too wide) in paragraph at lines 4608--4609
[][] 
[137 <./static_site_docker.png> <./instructors_code.png>] [138]
Chapter 25.
No file cyverse-container-camp-workshop-2019.ind.
[139] (./cyverse-container-camp-workshop-2019.aux)

Package rerunfilecheck Warning: File `cyverse-container-camp-workshop-2019.out'
 has changed.
(rerunfilecheck)                Rerun to get outlines right
(rerunfilecheck)                or use package `bookmark'.


LaTeX Warning: There were undefined references.


LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.

 )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi5.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsf
onts/cm/cmsy5.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrb8a
.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/urw/courier/ucrro8a.pfb></usr/share/texlive/
texmf-dist/fonts/type1/urw/helvetic/uhvb8a.pfb></usr/share/texlive/texmf-dist/f
onts/type1/urw/helvetic/uhvbo8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/
urw/helvetic/uhvr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/ut
mb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/
share/texlive/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on cyverse-container-camp-workshop-2019.pdf (143 pages, 9564322 
bytes).
Transcript written on cyverse-container-camp-workshop-2019.log.
Latexmk: Index file 'cyverse-container-camp-workshop-2019.idx' was written
Latexmk: Missing input file: 'cyverse-container-camp-workshop-2019.ind' from line
  'No file cyverse-container-camp-workshop-2019.ind.'
Latexmk: References changed.
Latexmk: References changed.
Latexmk: Log file says output to 'cyverse-container-camp-workshop-2019.pdf'
Latexmk: Log file says output to 'cyverse-container-camp-workshop-2019.pdf'
Rule 'makeindex cyverse-container-camp-workshop-2019.idx': File changes, etc:
   Non-existent destination files:
      'cyverse-container-camp-workshop-2019.ind'
------------
Run number 1 of rule 'makeindex cyverse-container-camp-workshop-2019.idx'
------------
------------
Running 'makeindex -s python.ist  -o "cyverse-container-camp-workshop-2019.ind" "cyverse-container-camp-workshop-2019.idx"'
------------
Latexmk: applying rule 'makeindex cyverse-container-camp-workshop-2019.idx'...
This is makeindex, version 2.15 [TeX Live 2017] (kpathsea + Thai support).
Scanning style file ./python.ist.......done (7 attributes redefined, 0 ignored).
Scanning input file cyverse-container-camp-workshop-2019.idx...done (0 entries accepted, 0 rejected).
Nothing written in cyverse-container-camp-workshop-2019.ind.
Transcript written in cyverse-container-camp-workshop-2019.ilg.
Rule 'pdflatex': File changes, etc:
   Changed files, or newly in use since previous run(s):
      'cyverse-container-camp-workshop-2019.aux'
      'cyverse-container-camp-workshop-2019.ind'
------------
Run number 2 of rule 'pdflatex'
------------
------------
Running 'pdflatex   -interaction=nonstopmode -recorder --jobname="cyverse-container-camp-workshop-2019"  "CyVerseDocumentation.tex"'
------------
Latexmk: applying rule 'pdflatex'...
This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./CyVerseDocumentation.tex
LaTeX2e <2017-04-15>
Babel <3.18> and hyphenation patterns for 84 language(s) loaded.
(./sphinxmanual.cls
Document Class: sphinxmanual 2018/12/22 v1.8.3 Document class (Sphinx manual)
(/usr/share/texlive/texmf-dist/tex/latex/base/report.cls
Document Class: report 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)))
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)))
(/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)<<t1.cmap>>)
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty
For additional information on amsmath, use the `?' option.
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty))
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty)
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty))
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty))
(/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty
(/usr/share/texlive/texmf-dist/tex/generic/babel/switch.def)
(/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf
(/usr/share/texlive/texmf-dist/tex/generic/babel/babel.def
(/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def))))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/fncychap/fncychap.sty) (./sphinx.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))
(/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu)))
(/usr/share/texlive/texmf-dist/tex/latex/titlesec/titlesec.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tabulary/tabulary.sty
(/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty))
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/varwidth/varwidth.sty)
(./sphinxmulticell.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty)
(/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty
Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix 
<2008/02/07> (tvz)) (./footnotehyper-sphinx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/float/float.sty)
(/usr/share/texlive/texmf-dist/tex/latex/wrapfig/wrapfig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty)
(/usr/share/texlive/texmf-dist/tex/latex/capt-of/capt-of.sty)
(/usr/share/texlive/texmf-dist/tex/latex/needspace/needspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/carlisle/remreset.sty)
(./sphinxhighlight.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty)
Writing index file cyverse-container-camp-workshop-2019.idx
(./cyverse-container-camp-workshop-2019.aux)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./cyverse-container-camp-workshop-2019.out)
(./cyverse-container-camp-workshop-2019.out)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)<<ot1.cmap>><<oml.cmap
>><<oms.cmap>><<omx.cmap>>
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd)
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}] [2]
(./cyverse-container-camp-workshop-2019.toc [1]) [2]
Overfull \hbox (132.49107pt too wide) in paragraph at lines 83--84
[][] 
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [1 <./cc-main.png> <
./cyverse_rgb1.png>] [2]
Chapter 1.
[3] [4]
Chapter 2.
[5]
Underfull \hbox (badness 5189) in paragraph at lines 2--288
[][][]\T1/ptm/m/n/10 Download Cy-Verse Cy-ber-
[6]
Chapter 3.

Underfull \hbox (badness 5802) in paragraph at lines 332--333
[]|\T1/ptm/m/n/10 General in-tro-duc-tion to

Underfull \hbox (badness 6675) in paragraph at lines 339--340
\T1/ptm/m/n/10 tainer tech-nol-ogy land-

Underfull \hbox (badness 10000) in paragraph at lines 353--354
[]|\T1/ptm/m/n/10 Introduction to Docker

Underfull \hbox (badness 6412) in paragraph at lines 360--361
[]|\T1/ptm/m/n/10 Lunch break (on your

Underfull \hbox (badness 10000) in paragraph at lines 379--380
[]|\T1/ptm/m/n/10 Docker hands-on ex-er-

Underfull \hbox (badness 10000) in paragraph at lines 2--383
[]|[][]\T1/ptm/m/n/10 Docker hands-on ex-er-

Underfull \hbox (badness 6961) in paragraph at lines 400--401
[]|\T1/ptm/m/n/10 Review Day 1 (Ques-

Underfull \hbox (badness 10000) in paragraph at lines 2--421
[][][]\T1/ptm/m/n/10 Non-interactive

Underfull \hbox (badness 10000) in paragraph at lines 1--441
[][][]$\T1/ptm/m/n/10 https : / / mirrorlab .

Underfull \hbox (badness 10000) in paragraph at lines 1--444
[][][]$\T1/ptm/m/n/10 https : / / it . arizona .

Underfull \hbox (badness 10000) in paragraph at lines 1--444
\T1/ptm/m/n/10 edu / service /

Overfull \hbox (38.81021pt too wide) in paragraph at lines 1--444
\T1/ptm/m/n/10 high-[]performance-[]computing$[][] 

Underfull \hbox (badness 5832) in paragraph at lines 462--463
[]|\T1/ptm/m/n/10 500k con-tain-ers a day

Underfull \hbox (badness 10000) in paragraph at lines 462--463
\T1/ptm/m/n/10 - Re-mote Pre-sen-ta-tion

Underfull \hbox (badness 10000) in paragraph at lines 2--480
[][][]\T1/ptm/m/n/10 Singularity in-tro-

Underfull \hbox (badness 10000) in paragraph at lines 2--483
[][][]\T1/ptm/m/n/10 Singularity in-tro-

Underfull \hbox (badness 10000) in paragraph at lines 494--495
[]|\T1/ptm/m/n/10 Advanced Sin-gu-lar-ity
[7]
Overfull \vbox (237.30956pt too high) has occurred while \output is active
[8]
Chapter 4.
[9] [10]
Chapter 5.
[11] [12]
Chapter 6.
[13] [14]
Chapter 7.
[15] [16]
Chapter 8.
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [17 <./docker.png>]
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [18] [19] [20]
[21] [22] [23]
Underfull \hbox (badness 10000) in paragraph at lines 1041--1043
\T1/ptm/b/n/10 Note:  \T1/ptm/m/n/10 When you run the \T1/pcr/m/n/10 docker bui
ld \T1/ptm/m/n/10 com-mand given be-low, make sure to re-place
[24]
Overfull \vbox (11.24115pt too high) detected at line 1126
[25] [26] [27] [28] [29] [30 <./portainer_demo.png>] [31 <./pwd.png>] [32]
Chapter 9.
[33] [34] [35 <./docker_image.png>] [36 <./private_registry.png>] [37]
Overfull \hbox (132.49107pt too wide) in paragraph at lines 1699--1700
[][] 

Overfull \hbox (132.49107pt too wide) in paragraph at lines 1710--1711
[][] 
[38 <./dockerhub_create.png>]
Overfull \hbox (132.49107pt too wide) in paragraph at lines 1724--1725
[][] 
[39 <./dockerhub_createrepo.png>]
Overfull \hbox (132.49107pt too wide) in paragraph at lines 1728--1729
[][] 
[40 <./dockerhub_buildsettings.png>] [41 <./dockerhub_autobuild.png>] [42 <./cr
eate_repo.png> <./create_repo2.png>]
Overfull \hbox (132.49107pt too wide) in paragraph at lines 1832--1833
[][] 
[43]
Overfull \vbox (90.47859pt too high) has occurred while \output is active
[44 <./dockerhub_autobuilds.png>] [45 <./auto_build-2.1.png>] [46 <./auto_build
-5.png> <./auto_build-6.png>] [47 <./auto_build-7.png>] [48 <./volumes.png>]
Underfull \hbox (badness 10000) in paragraph at lines 2050--2052
\T1/ptm/b/n/10 Note:  \T1/ptm/m/n/10 File lo-ca-tion on Mac OS X is a bit dif-f
er-ent: [][]$https : / / timonweb . com / posts /
[49] [50] [51 <./bind_mount.png>] [52] [53] [54] [55 <./dc-1.png>] [56]
Chapter 10.

Overfull \hbox (57.21031pt too wide) in paragraph at lines 2429--2430
[][] 
[57 <./fastqe.png>] [58] [59]
Overfull \vbox (9.74088pt too high) detected at line 2581
[60]
Overfull \hbox (57.20003pt too wide) in paragraph at lines 2593--2594
| []|  

Underfull \hbox (badness 10000) in paragraph at lines 2595--2596
[]\T1/ptm/m/n/10 You should be greeted by your own con-tainer-ised Jupyter ser-
vice! Now open \T1/pcr/m/n/10 galaxy/

Overfull \hbox (57.22421pt too wide) in paragraph at lines 2597--2598
| []|  
[61 <./jn_login1.png>] [62 <./jn_galaxy.png>]
Chapter 11.
[63 <./singularity.png>]
Overfull \hbox (132.49107pt too wide) in paragraph at lines 2647--2648
[][] 
[64 <./singularity-2.4-flow.png>]
Overfull \hbox (70.24437pt too wide) in paragraph at lines 2720--2720
[][]\T1/pcr/m/n/9 [[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=
[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]
=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][
]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[]
[]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[
][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=
[][]=[][]=[][]=[][]=[][]][][] 
[65]
Underfull \vbox (badness 1874) detected at line 2816
[66] [67]
Overfull \hbox (70.24437pt too wide) in paragraph at lines 2864--2864
[][]\T1/pcr/m/n/9 [[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=
[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]
=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][
]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[]
[]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[
][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=
[][]=[][]=[][]=[][]=[][]][][] 

Overfull \hbox (70.24437pt too wide) in paragraph at lines 2872--2872
[][]\T1/pcr/m/n/9 [[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=
[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]
=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][
]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[]
[]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[
][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=
[][]=[][]=[][]=[][]=[][]][][] 
[68]
Overfull \hbox (86.44435pt too wide) in paragraph at lines 2916--2916
[][]\T1/pcr/m/n/9 [[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=
[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]
=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][
]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[]
[]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[
][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=
[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]][][] 
[69] [70] [71] [72]
Chapter 12.
[73] [74] [75] [76]
Chapter 13.
[77]
Overfull \vbox (6.28346pt too high) detected at line 3399
[78] [79] [80] [81] [82]
Chapter 14.

Underfull \hbox (badness 10000) in paragraph at lines 3508--3509
\T1/ptm/m/n/10 Biocontainers for con-tainer camp by Amanda Cook-sey - [][]$http
s : / / de . cyverse . org / dl / d /
[83] [84]
Chapter 15.

Overfull \hbox (132.49107pt too wide) in paragraph at lines 3521--3522
[] 
[85] [86 <./dff16156a2fac35ba7650c7bae20c561e0b8d2e8.png>] [87] [88]
Chapter 16.

Overfull \hbox (57.21031pt too wide) in paragraph at lines 3572--3573
[] 
[89 <./snakemake.png>] [90]
Chapter 17.
[91]

! Package inputenc Error: Unicode char   (U+200A)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.3655 ...your version of Linux/Windows/OSX/OS9 
                                                  — well this is where D...


! Package inputenc Error: Unicode char   (U+200A)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.3655 ...ersion of Linux/Windows/OSX/OS9 — 
                                                  well this is where Docker ...


Overfull \hbox (57.21031pt too wide) in paragraph at lines 3668--3669
[][] 

Overfull \hbox (57.21031pt too wide) in paragraph at lines 3672--3673
[][] 
[92 <./jn_login.png>]
Overfull \hbox (57.21031pt too wide) in paragraph at lines 3676--3677
[][] 

Overfull \hbox (57.21031pt too wide) in paragraph at lines 3678--3679
[][] 
[93 <./jn_login2.png> <./jn_login3.png>]

! Package inputenc Error: Unicode char   (U+200A)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.3698 ...r compose file. And there you have it 
                                                  — a quick and easy way...


! Package inputenc Error: Unicode char   (U+200A)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.3698 ...ose file. And there you have it — 
                                                  a quick and easy way to st...


Overfull \hbox (57.21031pt too wide) in paragraph at lines 3705--3706
[][] 
[94 <./jn_login3.5.png>]
Overfull \hbox (57.21031pt too wide) in paragraph at lines 3713--3714
[][] 
[95 <./rstudio_ss.png> <./rstudio_login2.png>]
Overfull \hbox (57.21031pt too wide) in paragraph at lines 3719--3720
[][] 

! Package inputenc Error: Unicode char   (U+200A)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.3755 ...sphinxupquote{requirements.txt}} file 
                                                  — Contains python modu...


! Package inputenc Error: Unicode char   (U+200A)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.3755 ...upquote{requirements.txt}} file — 
                                                  Contains python modules an...


! Package inputenc Error: Unicode char   (U+200A)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.3770 ...inxupquote{app.py}} inside the folder 
                                                  — \sphinxcode{\sphinxupq...

[96 <./rstudio_login.png>] [97] [98] [99 <./cyverse_rgb.png>] [100]
Chapter 18.

Overfull \hbox (57.2353pt too wide) in paragraph at lines 3970--3971
[][] 
[101]
Overfull \hbox (57.2342pt too wide) in paragraph at lines 3995--3996
[][] 
[102 <./atmo-1.1.png>]
Overfull \hbox (57.21959pt too wide) in paragraph at lines 4014--4015
[][] 
[103 <./atmo_cp.png>]
Overfull \hbox (57.20882pt too wide) in paragraph at lines 4021--4022
[][] 
[104 <./atmo_launch0.png> <./atmo_launch1.png>]
Overfull \hbox (57.22607pt too wide) in paragraph at lines 4031--4032
[][] 

Overfull \hbox (57.23694pt too wide) in paragraph at lines 4041--4042
[][] 
[105 <./atmo_launch.png>]
Overfull \hbox (57.22354pt too wide) in paragraph at lines 4061--4062
[][] 
[106 <./atmo-6.png>]
Overfull \hbox (57.21503pt too wide) in paragraph at lines 4070--4071
[][] 
[107 <./atmo-8.png>] [108 <./atmo-9.png>]
Chapter 19.

Overfull \hbox (57.21031pt too wide) in paragraph at lines 4085--4086
[][] 
[109 <./f1000.png>]
Overfull \hbox (57.21031pt too wide) in paragraph at lines 4150--4151
[][] 

Overfull \hbox (57.21031pt too wide) in paragraph at lines 4154--4155
[][] 
[110 <./auto-1.png>]
Overfull \hbox (57.21031pt too wide) in paragraph at lines 4158--4159
[][] 
[111 <./auto-2.png>]
Overfull \hbox (57.21031pt too wide) in paragraph at lines 4162--4163
[][] 
[112 <./auto-3.png>]
Overfull \hbox (57.21031pt too wide) in paragraph at lines 4225--4226
[][] 
[113 <./auto-4.png>]
Overfull \hbox (57.21031pt too wide) in paragraph at lines 4250--4251
[][] 
[114 <./img_building_1.png>]
Overfull \hbox (57.21031pt too wide) in paragraph at lines 4258--4259
[][] 
[115 <./img_building_4.png> <./img_building_3.png>]
Overfull \hbox (57.21031pt too wide) in paragraph at lines 4277--4278
[][] 

Overfull \hbox (57.21031pt too wide) in paragraph at lines 4288--4289
[][] 
[116 <./img_building_9.png> <./img_building_5.png>]
Overfull \hbox (57.21031pt too wide) in paragraph at lines 4299--4300
[][] 
[117 <./img_building_6.png> <./img_building_8.png>] [118]
Chapter 20.

Overfull \hbox (57.20361pt too wide) in paragraph at lines 4329--4330
[][] 
[119]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 4336--4337
[][] 
[120 <./jupyter1-1.png>]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 4338--4339
[][] 
[121 <./jupyter1-2.png> <./jupyter1-3.png>]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 4349--4350
[][] 

Overfull \hbox (57.20361pt too wide) in paragraph at lines 4353--4354
[][] 
[122 <./jupyter1-9.png>]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 4372--4373
[][] 
[123 <./jupyter1-4.png>]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 4383--4384
[][] 
[124 <./jupyter1-5.png>]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 4390--4391
[][] 
[125 <./jupyter1-6.png>]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 4392--4393
[][] 
[126 <./jupyter1-7.png> <./jupyter1-8.png>] [127] [128]
Chapter 21.
[129] [130]
Chapter 22.
[131] [132]
Chapter 23.
[133] [134]
Chapter 24.
[135]
Overfull \hbox (94.8507pt too wide) in paragraph at lines 4604--4605
[][] 
[136]
Overfull \hbox (94.8507pt too wide) in paragraph at lines 4608--4609
[][] 
[137 <./static_site_docker.png> <./instructors_code.png>] [138]
Chapter 25.
(./cyverse-container-camp-workshop-2019.ind) [139]
(./cyverse-container-camp-workshop-2019.aux) )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi5.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsf
onts/cm/cmsy5.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrb8a
.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/urw/courier/ucrro8a.pfb></usr/share/texlive/
texmf-dist/fonts/type1/urw/helvetic/uhvb8a.pfb></usr/share/texlive/texmf-dist/f
onts/type1/urw/helvetic/uhvbo8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/
urw/helvetic/uhvr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/ut
mb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/
share/texlive/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on cyverse-container-camp-workshop-2019.pdf (143 pages, 9568610 
bytes).
Transcript written on cyverse-container-camp-workshop-2019.log.
Latexmk: Index file 'cyverse-container-camp-workshop-2019.idx' was written
Latexmk: Log file says output to 'cyverse-container-camp-workshop-2019.pdf'
Latexmk: Log file says output to 'cyverse-container-camp-workshop-2019.pdf'
Rule 'pdflatex': File changes, etc:
   Changed files, or newly in use since previous run(s):
      'cyverse-container-camp-workshop-2019.out'
      'cyverse-container-camp-workshop-2019.toc'
------------
Run number 3 of rule 'pdflatex'
------------
------------
Running 'pdflatex   -interaction=nonstopmode -recorder --jobname="cyverse-container-camp-workshop-2019"  "CyVerseDocumentation.tex"'
------------
Latexmk: applying rule 'pdflatex'...
This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./CyVerseDocumentation.tex
LaTeX2e <2017-04-15>
Babel <3.18> and hyphenation patterns for 84 language(s) loaded.
(./sphinxmanual.cls
Document Class: sphinxmanual 2018/12/22 v1.8.3 Document class (Sphinx manual)
(/usr/share/texlive/texmf-dist/tex/latex/base/report.cls
Document Class: report 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)))
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)))
(/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)<<t1.cmap>>)
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty
For additional information on amsmath, use the `?' option.
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty))
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty)
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty))
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty))
(/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty
(/usr/share/texlive/texmf-dist/tex/generic/babel/switch.def)
(/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf
(/usr/share/texlive/texmf-dist/tex/generic/babel/babel.def
(/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def))))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/fncychap/fncychap.sty) (./sphinx.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))
(/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu)))
(/usr/share/texlive/texmf-dist/tex/latex/titlesec/titlesec.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tabulary/tabulary.sty
(/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty))
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/varwidth/varwidth.sty)
(./sphinxmulticell.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty)
(/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty
Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix 
<2008/02/07> (tvz)) (./footnotehyper-sphinx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/float/float.sty)
(/usr/share/texlive/texmf-dist/tex/latex/wrapfig/wrapfig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty)
(/usr/share/texlive/texmf-dist/tex/latex/capt-of/capt-of.sty)
(/usr/share/texlive/texmf-dist/tex/latex/needspace/needspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/carlisle/remreset.sty)
(./sphinxhighlight.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty)
Writing index file cyverse-container-camp-workshop-2019.idx
(./cyverse-container-camp-workshop-2019.aux)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./cyverse-container-camp-workshop-2019.out)
(./cyverse-container-camp-workshop-2019.out)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)<<ot1.cmap>><<oml.cmap
>><<oms.cmap>><<omx.cmap>>
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd)
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}] [2]
(./cyverse-container-camp-workshop-2019.toc [1]) [2]
Overfull \hbox (132.49107pt too wide) in paragraph at lines 83--84
[][] 
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [1 <./cc-main.png> <
./cyverse_rgb1.png>] [2]
Chapter 1.
[3] [4]
Chapter 2.
[5]
Underfull \hbox (badness 5189) in paragraph at lines 2--288
[][][]\T1/ptm/m/n/10 Download Cy-Verse Cy-ber-
[6]
Chapter 3.

Underfull \hbox (badness 5802) in paragraph at lines 332--333
[]|\T1/ptm/m/n/10 General in-tro-duc-tion to

Underfull \hbox (badness 6675) in paragraph at lines 339--340
\T1/ptm/m/n/10 tainer tech-nol-ogy land-

Underfull \hbox (badness 10000) in paragraph at lines 353--354
[]|\T1/ptm/m/n/10 Introduction to Docker

Underfull \hbox (badness 6412) in paragraph at lines 360--361
[]|\T1/ptm/m/n/10 Lunch break (on your

Underfull \hbox (badness 10000) in paragraph at lines 379--380
[]|\T1/ptm/m/n/10 Docker hands-on ex-er-

Underfull \hbox (badness 10000) in paragraph at lines 2--383
[]|[][]\T1/ptm/m/n/10 Docker hands-on ex-er-

Underfull \hbox (badness 6961) in paragraph at lines 400--401
[]|\T1/ptm/m/n/10 Review Day 1 (Ques-

Underfull \hbox (badness 10000) in paragraph at lines 2--421
[][][]\T1/ptm/m/n/10 Non-interactive

Underfull \hbox (badness 10000) in paragraph at lines 1--441
[][][]$\T1/ptm/m/n/10 https : / / mirrorlab .

Underfull \hbox (badness 10000) in paragraph at lines 1--444
[][][]$\T1/ptm/m/n/10 https : / / it . arizona .

Underfull \hbox (badness 10000) in paragraph at lines 1--444
\T1/ptm/m/n/10 edu / service /

Overfull \hbox (38.81021pt too wide) in paragraph at lines 1--444
\T1/ptm/m/n/10 high-[]performance-[]computing$[][] 

Underfull \hbox (badness 5832) in paragraph at lines 462--463
[]|\T1/ptm/m/n/10 500k con-tain-ers a day

Underfull \hbox (badness 10000) in paragraph at lines 462--463
\T1/ptm/m/n/10 - Re-mote Pre-sen-ta-tion

Underfull \hbox (badness 10000) in paragraph at lines 2--480
[][][]\T1/ptm/m/n/10 Singularity in-tro-

Underfull \hbox (badness 10000) in paragraph at lines 2--483
[][][]\T1/ptm/m/n/10 Singularity in-tro-

Underfull \hbox (badness 10000) in paragraph at lines 494--495
[]|\T1/ptm/m/n/10 Advanced Sin-gu-lar-ity
[7]
Overfull \vbox (237.30956pt too high) has occurred while \output is active
[8]
Chapter 4.
[9] [10]
Chapter 5.
[11] [12]
Chapter 6.
[13] [14]
Chapter 7.
[15] [16]
Chapter 8.
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [17 <./docker.png>]
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [18] [19] [20]
[21] [22] [23]
Underfull \hbox (badness 10000) in paragraph at lines 1041--1043
\T1/ptm/b/n/10 Note:  \T1/ptm/m/n/10 When you run the \T1/pcr/m/n/10 docker bui
ld \T1/ptm/m/n/10 com-mand given be-low, make sure to re-place
[24]
Overfull \vbox (11.24115pt too high) detected at line 1126
[25] [26] [27] [28] [29] [30 <./portainer_demo.png>] [31 <./pwd.png>] [32]
Chapter 9.
[33] [34] [35 <./docker_image.png>] [36 <./private_registry.png>] [37]
Overfull \hbox (132.49107pt too wide) in paragraph at lines 1699--1700
[][] 

Overfull \hbox (132.49107pt too wide) in paragraph at lines 1710--1711
[][] 
[38 <./dockerhub_create.png>]
Overfull \hbox (132.49107pt too wide) in paragraph at lines 1724--1725
[][] 
[39 <./dockerhub_createrepo.png>]
Overfull \hbox (132.49107pt too wide) in paragraph at lines 1728--1729
[][] 
[40 <./dockerhub_buildsettings.png>] [41 <./dockerhub_autobuild.png>] [42 <./cr
eate_repo.png> <./create_repo2.png>]
Overfull \hbox (132.49107pt too wide) in paragraph at lines 1832--1833
[][] 
[43]
Overfull \vbox (90.47859pt too high) has occurred while \output is active
[44 <./dockerhub_autobuilds.png>] [45 <./auto_build-2.1.png>] [46 <./auto_build
-5.png> <./auto_build-6.png>] [47 <./auto_build-7.png>] [48 <./volumes.png>]
Underfull \hbox (badness 10000) in paragraph at lines 2050--2052
\T1/ptm/b/n/10 Note:  \T1/ptm/m/n/10 File lo-ca-tion on Mac OS X is a bit dif-f
er-ent: [][]$https : / / timonweb . com / posts /
[49] [50] [51 <./bind_mount.png>] [52] [53] [54] [55 <./dc-1.png>] [56]
Chapter 10.

Overfull \hbox (57.21031pt too wide) in paragraph at lines 2429--2430
[][] 
[57 <./fastqe.png>] [58] [59]
Overfull \vbox (9.74088pt too high) detected at line 2581
[60]
Overfull \hbox (57.20003pt too wide) in paragraph at lines 2593--2594
| []|  

Underfull \hbox (badness 10000) in paragraph at lines 2595--2596
[]\T1/ptm/m/n/10 You should be greeted by your own con-tainer-ised Jupyter ser-
vice! Now open \T1/pcr/m/n/10 galaxy/

Overfull \hbox (57.22421pt too wide) in paragraph at lines 2597--2598
| []|  
[61 <./jn_login1.png>] [62 <./jn_galaxy.png>]
Chapter 11.
[63 <./singularity.png>]
Overfull \hbox (132.49107pt too wide) in paragraph at lines 2647--2648
[][] 
[64 <./singularity-2.4-flow.png>]
Overfull \hbox (70.24437pt too wide) in paragraph at lines 2720--2720
[][]\T1/pcr/m/n/9 [[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=
[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]
=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][
]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[]
[]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[
][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=
[][]=[][]=[][]=[][]=[][]][][] 
[65]
Underfull \vbox (badness 1874) detected at line 2816
[66] [67]
Overfull \hbox (70.24437pt too wide) in paragraph at lines 2864--2864
[][]\T1/pcr/m/n/9 [[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=
[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]
=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][
]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[]
[]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[
][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=
[][]=[][]=[][]=[][]=[][]][][] 

Overfull \hbox (70.24437pt too wide) in paragraph at lines 2872--2872
[][]\T1/pcr/m/n/9 [[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=
[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]
=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][
]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[]
[]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[
][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=
[][]=[][]=[][]=[][]=[][]][][] 
[68]
Overfull \hbox (86.44435pt too wide) in paragraph at lines 2916--2916
[][]\T1/pcr/m/n/9 [[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=
[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]
=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][
]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[]
[]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[
][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]=
[][]=[][]=[][]=[][]=[][]=[][]=[][]=[][]][][] 
[69] [70] [71] [72]
Chapter 12.
[73] [74] [75] [76]
Chapter 13.
[77]
Overfull \vbox (6.28346pt too high) detected at line 3399
[78] [79] [80] [81] [82]
Chapter 14.

Underfull \hbox (badness 10000) in paragraph at lines 3508--3509
\T1/ptm/m/n/10 Biocontainers for con-tainer camp by Amanda Cook-sey - [][]$http
s : / / de . cyverse . org / dl / d /
[83] [84]
Chapter 15.

Overfull \hbox (132.49107pt too wide) in paragraph at lines 3521--3522
[] 
[85] [86 <./dff16156a2fac35ba7650c7bae20c561e0b8d2e8.png>] [87] [88]
Chapter 16.

Overfull \hbox (57.21031pt too wide) in paragraph at lines 3572--3573
[] 
[89 <./snakemake.png>] [90]
Chapter 17.
[91]

! Package inputenc Error: Unicode char   (U+200A)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.3655 ...your version of Linux/Windows/OSX/OS9 
                                                  — well this is where D...


! Package inputenc Error: Unicode char   (U+200A)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.3655 ...ersion of Linux/Windows/OSX/OS9 — 
                                                  well this is where Docker ...


Overfull \hbox (57.21031pt too wide) in paragraph at lines 3668--3669
[][] 

Overfull \hbox (57.21031pt too wide) in paragraph at lines 3672--3673
[][] 
[92 <./jn_login.png>]
Overfull \hbox (57.21031pt too wide) in paragraph at lines 3676--3677
[][] 

Overfull \hbox (57.21031pt too wide) in paragraph at lines 3678--3679
[][] 
[93 <./jn_login2.png> <./jn_login3.png>]

! Package inputenc Error: Unicode char   (U+200A)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.3698 ...r compose file. And there you have it 
                                                  — a quick and easy way...


! Package inputenc Error: Unicode char   (U+200A)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.3698 ...ose file. And there you have it — 
                                                  a quick and easy way to st...


Overfull \hbox (57.21031pt too wide) in paragraph at lines 3705--3706
[][] 
[94 <./jn_login3.5.png>]
Overfull \hbox (57.21031pt too wide) in paragraph at lines 3713--3714
[][] 
[95 <./rstudio_ss.png> <./rstudio_login2.png>]
Overfull \hbox (57.21031pt too wide) in paragraph at lines 3719--3720
[][] 

! Package inputenc Error: Unicode char   (U+200A)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.3755 ...sphinxupquote{requirements.txt}} file 
                                                  — Contains python modu...


! Package inputenc Error: Unicode char   (U+200A)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.3755 ...upquote{requirements.txt}} file — 
                                                  Contains python modules an...


! Package inputenc Error: Unicode char   (U+200A)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.3770 ...inxupquote{app.py}} inside the folder 
                                                  — \sphinxcode{\sphinxupq...

[96 <./rstudio_login.png>] [97] [98] [99 <./cyverse_rgb.png>] [100]
Chapter 18.

Overfull \hbox (57.2353pt too wide) in paragraph at lines 3970--3971
[][] 
[101]
Overfull \hbox (57.2342pt too wide) in paragraph at lines 3995--3996
[][] 
[102 <./atmo-1.1.png>]
Overfull \hbox (57.21959pt too wide) in paragraph at lines 4014--4015
[][] 
[103 <./atmo_cp.png>]
Overfull \hbox (57.20882pt too wide) in paragraph at lines 4021--4022
[][] 
[104 <./atmo_launch0.png> <./atmo_launch1.png>]
Overfull \hbox (57.22607pt too wide) in paragraph at lines 4031--4032
[][] 

Overfull \hbox (57.23694pt too wide) in paragraph at lines 4041--4042
[][] 
[105 <./atmo_launch.png>]
Overfull \hbox (57.22354pt too wide) in paragraph at lines 4061--4062
[][] 
[106 <./atmo-6.png>]
Overfull \hbox (57.21503pt too wide) in paragraph at lines 4070--4071
[][] 
[107 <./atmo-8.png>] [108 <./atmo-9.png>]
Chapter 19.

Overfull \hbox (57.21031pt too wide) in paragraph at lines 4085--4086
[][] 
[109 <./f1000.png>]
Overfull \hbox (57.21031pt too wide) in paragraph at lines 4150--4151
[][] 

Overfull \hbox (57.21031pt too wide) in paragraph at lines 4154--4155
[][] 
[110 <./auto-1.png>]
Overfull \hbox (57.21031pt too wide) in paragraph at lines 4158--4159
[][] 
[111 <./auto-2.png>]
Overfull \hbox (57.21031pt too wide) in paragraph at lines 4162--4163
[][] 
[112 <./auto-3.png>]
Overfull \hbox (57.21031pt too wide) in paragraph at lines 4225--4226
[][] 
[113 <./auto-4.png>]
Overfull \hbox (57.21031pt too wide) in paragraph at lines 4250--4251
[][] 
[114 <./img_building_1.png>]
Overfull \hbox (57.21031pt too wide) in paragraph at lines 4258--4259
[][] 
[115 <./img_building_4.png> <./img_building_3.png>]
Overfull \hbox (57.21031pt too wide) in paragraph at lines 4277--4278
[][] 

Overfull \hbox (57.21031pt too wide) in paragraph at lines 4288--4289
[][] 
[116 <./img_building_9.png> <./img_building_5.png>]
Overfull \hbox (57.21031pt too wide) in paragraph at lines 4299--4300
[][] 
[117 <./img_building_6.png> <./img_building_8.png>] [118]
Chapter 20.

Overfull \hbox (57.20361pt too wide) in paragraph at lines 4329--4330
[][] 
[119]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 4336--4337
[][] 
[120 <./jupyter1-1.png>]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 4338--4339
[][] 
[121 <./jupyter1-2.png> <./jupyter1-3.png>]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 4349--4350
[][] 

Overfull \hbox (57.20361pt too wide) in paragraph at lines 4353--4354
[][] 
[122 <./jupyter1-9.png>]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 4372--4373
[][] 
[123 <./jupyter1-4.png>]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 4383--4384
[][] 
[124 <./jupyter1-5.png>]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 4390--4391
[][] 
[125 <./jupyter1-6.png>]
Overfull \hbox (57.20361pt too wide) in paragraph at lines 4392--4393
[][] 
[126 <./jupyter1-7.png> <./jupyter1-8.png>] [127] [128]
Chapter 21.
[129] [130]
Chapter 22.
[131] [132]
Chapter 23.
[133] [134]
Chapter 24.
[135]
Overfull \hbox (94.8507pt too wide) in paragraph at lines 4604--4605
[][] 
[136]
Overfull \hbox (94.8507pt too wide) in paragraph at lines 4608--4609
[][] 
[137 <./static_site_docker.png> <./instructors_code.png>] [138]
Chapter 25.
(./cyverse-container-camp-workshop-2019.ind) [139]
(./cyverse-container-camp-workshop-2019.aux) )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi5.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsf
onts/cm/cmsy5.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrb8a
.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/urw/courier/ucrro8a.pfb></usr/share/texlive/
texmf-dist/fonts/type1/urw/helvetic/uhvb8a.pfb></usr/share/texlive/texmf-dist/f
onts/type1/urw/helvetic/uhvbo8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/
urw/helvetic/uhvr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/ut
mb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/
share/texlive/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on cyverse-container-camp-workshop-2019.pdf (143 pages, 9568610 
bytes).
Transcript written on cyverse-container-camp-workshop-2019.log.
Latexmk: Index file 'cyverse-container-camp-workshop-2019.idx' was written
Latexmk: Log file says output to 'cyverse-container-camp-workshop-2019.pdf'
Latexmk: Log file says output to 'cyverse-container-camp-workshop-2019.pdf'
Collected error summary (may duplicate other messages):
  pdflatex: Command for 'pdflatex' gave return code 256
Latexmk: Errors, in force_mode: so I tried finishing targets

[rtd-command-info] start-time: 2019-07-17T18:02:13.606541Z, end-time: 2019-07-17T18:02:13.936820Z, duration: 0, exit-code: 0
mv -f /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/./_build/latex/cyverse-container-camp-workshop-2019.pdf /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/artifacts/latest/sphinx_pdf/cyverse-container-camp-workshop-2019.pdf


[rtd-command-info] start-time: 2019-07-17T18:02:14.203220Z, end-time: 2019-07-17T18:02:39.279954Z, duration: 25, exit-code: 0
python sphinx-build -T -b epub -d _build/doctrees-epub -D language=en . _build/epub
Running Sphinx v1.8.5
loading translations [en]... done
making output directory...
loading pickled environment... done
building [mo]: targets for 0 po files that are out of date
building [epub]: targets for 55 source files that are out of date
updating environment: 55 added, 0 changed, 0 removed
reading sources... [  1%] breakout/biocontainers
reading sources... [  3%] breakout/datascience
reading sources... [  5%] breakout/nvidia-docker
reading sources... [  7%] breakout/workflows
reading sources... [  9%] buildenv/lib/python3.5/site-packages/Babel-2.5.3.dist-info/DESCRIPTION
reading sources... [ 10%] buildenv/lib/python3.5/site-packages/CommonMark-0.5.4.dist-info/DESCRIPTION
reading sources... [ 12%] buildenv/lib/python3.5/site-packages/Jinja2-2.10.dist-info/DESCRIPTION
reading sources... [ 14%] buildenv/lib/python3.5/site-packages/MarkupSafe-1.0.dist-info/DESCRIPTION
reading sources... [ 16%] buildenv/lib/python3.5/site-packages/Pygments-2.2.0.dist-info/DESCRIPTION
reading sources... [ 18%] buildenv/lib/python3.5/site-packages/Sphinx-1.6.6.dist-info/DESCRIPTION
reading sources... [ 20%] buildenv/lib/python3.5/site-packages/alabaster-0.7.10.dist-info/DESCRIPTION
reading sources... [ 21%] buildenv/lib/python3.5/site-packages/certifi-2018.1.18.dist-info/DESCRIPTION
reading sources... [ 23%] buildenv/lib/python3.5/site-packages/chardet-3.0.4.dist-info/DESCRIPTION
reading sources... [ 25%] buildenv/lib/python3.5/site-packages/docutils-0.14.dist-info/DESCRIPTION
reading sources... [ 27%] buildenv/lib/python3.5/site-packages/guzzle_sphinx_theme-0.7.11.dist-info/DESCRIPTION
reading sources... [ 29%] buildenv/lib/python3.5/site-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/README
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages/recommonmark/parser.py:65: UserWarning: Container node skipped: type=document
  warn("Container node skipped: type={0}".format(mdnode.t))
reading sources... [ 30%] buildenv/lib/python3.5/site-packages/idna-2.6.dist-info/DESCRIPTION
reading sources... [ 32%] buildenv/lib/python3.5/site-packages/imagesize-0.7.1.dist-info/DESCRIPTION
reading sources... [ 34%] buildenv/lib/python3.5/site-packages/pip-9.0.1.dist-info/DESCRIPTION
reading sources... [ 36%] buildenv/lib/python3.5/site-packages/pytz-2017.3.dist-info/DESCRIPTION
reading sources... [ 38%] buildenv/lib/python3.5/site-packages/recommonmark-0.4.0.dist-info/DESCRIPTION
reading sources... [ 40%] buildenv/lib/python3.5/site-packages/requests-2.18.4.dist-info/DESCRIPTION
reading sources... [ 41%] buildenv/lib/python3.5/site-packages/setuptools-38.4.0.dist-info/DESCRIPTION
reading sources... [ 43%] buildenv/lib/python3.5/site-packages/six-1.11.0.dist-info/DESCRIPTION
reading sources... [ 45%] buildenv/lib/python3.5/site-packages/snowballstemmer-1.2.1.dist-info/DESCRIPTION
reading sources... [ 47%] buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/base
reading sources... [ 49%] buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/class
reading sources... [ 50%] buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/module
reading sources... [ 52%] buildenv/lib/python3.5/site-packages/sphinx_bootstrap_theme-0.6.4.dist-info/DESCRIPTION
reading sources... [ 54%] buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/DESCRIPTION
reading sources... [ 56%] buildenv/lib/python3.5/site-packages/sphinxcontrib_images-0.7.0.dist-info/DESCRIPTION
reading sources... [ 58%] buildenv/lib/python3.5/site-packages/sphinxcontrib_websupport-1.0.1.dist-info/DESCRIPTION
reading sources... [ 60%] buildenv/lib/python3.5/site-packages/urllib3-1.22.dist-info/DESCRIPTION
reading sources... [ 61%] buildenv/lib/python3.5/site-packages/wheel-0.30.0.dist-info/DESCRIPTION
reading sources... [ 63%] cyverse/boot
reading sources... [ 65%] cyverse/de_docker
reading sources... [ 67%] cyverse/vice_docker
reading sources... [ 69%] docker/dockeradvanced
reading sources... [ 70%] docker/dockerhandson
reading sources... [ 72%] docker/dockerintro
reading sources... [ 74%] getting_started/about_cyverse
reading sources... [ 76%] getting_started/agenda
reading sources... [ 78%] getting_started/installation
reading sources... [ 80%] getting_started/main
reading sources... [ 81%] index
reading sources... [ 83%] instructions_reporting/instructors
reading sources... [ 85%] instructions_reporting/problems
reading sources... [ 87%] singularity/singularityadvanced
reading sources... [ 89%] singularity/singularityintro
reading sources... [ 90%] topics/breakout_session
reading sources... [ 92%] topics/train_docker
reading sources... [ 94%] topics/train_singularity
reading sources... [ 96%] useful_resources/usefulresources_docker
reading sources... [ 98%] useful_resources/usefulresources_other
reading sources... [100%] useful_resources/usefulresources_singularity

/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/breakout/biocontainers.rst:2: WARNING: Title underline too short.

**Biocontainers**
================
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/breakout/datascience.rst:2: WARNING: Duplicate explicit target name: "here".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/requests-2.18.4.dist-info/DESCRIPTION.rst:162: WARNING: Inline emphasis start-string without end-string.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/base.rst:3: WARNING: Error in "currentmodule" directive:
maximum 1 argument(s) allowed, 3 supplied.

.. currentmodule:: {{ module }}
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/class.rst:3: WARNING: Error in "currentmodule" directive:
maximum 1 argument(s) allowed, 3 supplied.

.. currentmodule:: {{ module }}
WARNING: invalid signature for autoclass (u'{{ objname }}')
WARNING: don't know which module to import for autodocumenting u'{{ objname }}' (try placing a "module" or "currentmodule" directive in the document, or giving an explicit module name)
WARNING: invalid signature for automodule (u'{{ fullname }}')
WARNING: don't know which module to import for autodocumenting u'{{ fullname }}' (try placing a "module" or "currentmodule" directive in the document, or giving an explicit module name)
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/DESCRIPTION.rst:: WARNING: image file not readable: buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/screen_mobile.png
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/cyverse/boot.rst:70: WARNING: Content block expected for the "important" directive; none found.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/cyverse/de_docker.rst:4: WARNING: Duplicate explicit target name: "dockerhub".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/cyverse/vice_docker.rst:4: WARNING: Duplicate explicit target name: "here".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockeradvanced.rst:2: WARNING: Duplicate explicit target name: "docker hub".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockeradvanced.rst:441: WARNING: Error in "code-block" directive:
maximum 1 argument(s) allowed, 3 supplied.

.. code-block:: bash
   -v /home/username/your_data_folder:/data:ro
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockeradvanced.rst:527: WARNING: Error in "code-block" directive:
1 argument(s) required, 0 supplied.

.. code-block::

        HOSTNAME=790e13bba28a
        SHLVL=1
        HOME=/root
        PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
        PWD=/
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockerhandson.rst:35: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockerintro.rst:501: WARNING: Duplicate explicit target name: "dockerfile".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockerintro.rst:557: WARNING: Duplicate explicit target name: "build the image".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockerintro.rst:594: WARNING: Duplicate explicit target name: "run your image".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockerintro.rst:473: WARNING: Duplicate target name, cannot be used as a unique reference: "build the image".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockerintro.rst:474: WARNING: Duplicate target name, cannot be used as a unique reference: "run your image".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/getting_started/agenda.rst:2: WARNING: Duplicate explicit target name: "slides".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/getting_started/main.rst:4: WARNING: Title underline too short.

**Workshop Code of Conduct and Other Information**
============================
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityadvanced.rst:7: WARNING: Title underline too short.

5.0 Building your own Containers from scratch
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityadvanced.rst:30: WARNING: Title underline too short.

5.2 Building Singularity containers
==================================
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityadvanced.rst:74: WARNING: Title underline too short.

5.2.1: Exercise (~30 minutes): Create a Singularity file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityadvanced.rst:74: WARNING: Title underline too short.

5.2.1: Exercise (~30 minutes): Create a Singularity file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityadvanced.rst:140: WARNING: Duplicate explicit target name: "user guide".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityadvanced.rst:278: WARNING: Error in "code-block" directive:
maximum 1 argument(s) allowed, 7 supplied.

.. code-block:: bash
  BootStrap: debootstrap
  OSVersion: xenial
  MirrorURL: http://us.archive.ubuntu.com/ubuntu/

  %runscript
      echo "This is what happens when you run the container..."

  %post
      echo "Hello from inside the container"
      sed -i 's/$/ universe/' /etc/apt/sources.list
      apt update
      apt -y --allow-unauthenticated install vim build-essential wget gfortran bison libibverbs-dev libibmad-dev libibumad-dev librdmacm-dev libmlx5-dev libmlx4-dev
      wget http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.1.tar.gz
      tar xvf mvapich2-2.1.tar.gz
      cd mvapich2-2.1
      ./configure --prefix=/usr/local
      make -j4
      make install
      /usr/local/bin/mpicc examples/hellow.c -o /usr/bin/hellow
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityintro.rst:2: WARNING: Duplicate explicit target name: "singularity".
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/Babel-2.5.3.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/CommonMark-0.5.4.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/Jinja2-2.10.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/MarkupSafe-1.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/Pygments-2.2.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/Sphinx-1.6.6.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/alabaster-0.7.10.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/certifi-2018.1.18.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/chardet-3.0.4.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/docutils-0.14.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/guzzle_sphinx_theme-0.7.11.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/README.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/idna-2.6.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/imagesize-0.7.1.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/pip-9.0.1.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/pytz-2017.3.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/recommonmark-0.4.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/requests-2.18.4.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/setuptools-38.4.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/six-1.11.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/snowballstemmer-1.2.1.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/base.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/class.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/module.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx_bootstrap_theme-0.6.4.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinxcontrib_images-0.7.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/sphinxcontrib_websupport-1.0.1.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/urllib3-1.22.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/buildenv/lib/python3.5/site-packages/wheel-0.30.0.dist-info/DESCRIPTION.rst: WARNING: document isn't included in any toctree
done
preparing documents... done
writing output... [  1%] breakout/biocontainers
writing output... [  3%] breakout/datascience
writing output... [  5%] breakout/nvidia-docker
writing output... [  7%] breakout/workflows
writing output... [  9%] buildenv/lib/python3.5/site-packages/Babel-2.5.3.dist-info/DESCRIPTION
writing output... [ 10%] buildenv/lib/python3.5/site-packages/CommonMark-0.5.4.dist-info/DESCRIPTION
writing output... [ 12%] buildenv/lib/python3.5/site-packages/Jinja2-2.10.dist-info/DESCRIPTION
writing output... [ 14%] buildenv/lib/python3.5/site-packages/MarkupSafe-1.0.dist-info/DESCRIPTION
writing output... [ 16%] buildenv/lib/python3.5/site-packages/Pygments-2.2.0.dist-info/DESCRIPTION
writing output... [ 18%] buildenv/lib/python3.5/site-packages/Sphinx-1.6.6.dist-info/DESCRIPTION
writing output... [ 20%] buildenv/lib/python3.5/site-packages/alabaster-0.7.10.dist-info/DESCRIPTION
writing output... [ 21%] buildenv/lib/python3.5/site-packages/certifi-2018.1.18.dist-info/DESCRIPTION
writing output... [ 23%] buildenv/lib/python3.5/site-packages/chardet-3.0.4.dist-info/DESCRIPTION
writing output... [ 25%] buildenv/lib/python3.5/site-packages/docutils-0.14.dist-info/DESCRIPTION
writing output... [ 27%] buildenv/lib/python3.5/site-packages/guzzle_sphinx_theme-0.7.11.dist-info/DESCRIPTION
writing output... [ 29%] buildenv/lib/python3.5/site-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/README
writing output... [ 30%] buildenv/lib/python3.5/site-packages/idna-2.6.dist-info/DESCRIPTION
writing output... [ 32%] buildenv/lib/python3.5/site-packages/imagesize-0.7.1.dist-info/DESCRIPTION
writing output... [ 34%] buildenv/lib/python3.5/site-packages/pip-9.0.1.dist-info/DESCRIPTION
writing output... [ 36%] buildenv/lib/python3.5/site-packages/pytz-2017.3.dist-info/DESCRIPTION
writing output... [ 38%] buildenv/lib/python3.5/site-packages/recommonmark-0.4.0.dist-info/DESCRIPTION
writing output... [ 40%] buildenv/lib/python3.5/site-packages/requests-2.18.4.dist-info/DESCRIPTION
writing output... [ 41%] buildenv/lib/python3.5/site-packages/setuptools-38.4.0.dist-info/DESCRIPTION
writing output... [ 43%] buildenv/lib/python3.5/site-packages/six-1.11.0.dist-info/DESCRIPTION
writing output... [ 45%] buildenv/lib/python3.5/site-packages/snowballstemmer-1.2.1.dist-info/DESCRIPTION
writing output... [ 47%] buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/base
writing output... [ 49%] buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/class
writing output... [ 50%] buildenv/lib/python3.5/site-packages/sphinx/ext/autosummary/templates/autosummary/module
writing output... [ 52%] buildenv/lib/python3.5/site-packages/sphinx_bootstrap_theme-0.6.4.dist-info/DESCRIPTION
writing output... [ 54%] buildenv/lib/python3.5/site-packages/sphinx_rtd_theme-0.2.4.dist-info/DESCRIPTION
writing output... [ 56%] buildenv/lib/python3.5/site-packages/sphinxcontrib_images-0.7.0.dist-info/DESCRIPTION
writing output... [ 58%] buildenv/lib/python3.5/site-packages/sphinxcontrib_websupport-1.0.1.dist-info/DESCRIPTION
writing output... [ 60%] buildenv/lib/python3.5/site-packages/urllib3-1.22.dist-info/DESCRIPTION
writing output... [ 61%] buildenv/lib/python3.5/site-packages/wheel-0.30.0.dist-info/DESCRIPTION
writing output... [ 63%] cyverse/boot
writing output... [ 65%] cyverse/de_docker
writing output... [ 67%] cyverse/vice_docker
writing output... [ 69%] docker/dockeradvanced
writing output... [ 70%] docker/dockerhandson
writing output... [ 72%] docker/dockerintro
writing output... [ 74%] getting_started/about_cyverse
writing output... [ 76%] getting_started/agenda
writing output... [ 78%] getting_started/installation
writing output... [ 80%] getting_started/main
writing output... [ 81%] index
writing output... [ 83%] instructions_reporting/instructors
writing output... [ 85%] instructions_reporting/problems
writing output... [ 87%] singularity/singularityadvanced
writing output... [ 89%] singularity/singularityintro
writing output... [ 90%] topics/breakout_session
writing output... [ 92%] topics/train_docker
writing output... [ 94%] topics/train_singularity
writing output... [ 96%] useful_resources/usefulresources_docker
writing output... [ 98%] useful_resources/usefulresources_other
writing output... [100%] useful_resources/usefulresources_singularity

/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/docker/dockeradvanced.rst:595: WARNING: Could not lex literal_block as "bash". Highlighting skipped.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityintro.rst:77: WARNING: Could not lex literal_block as "bash". Highlighting skipped.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityintro.rst:112: WARNING: Could not lex literal_block as "bash". Highlighting skipped.
generating indices... genindex
writing additional pages...
copying images... [  1%] https://raw.githubusercontent.com/requests/requests/master/docs/_static/requests-logo-small.png
copying images... [  2%] https://img.shields.io/badge/Say%20Thanks-!-1EAEDB.svg
copying images... [  3%] breakout/../img/rstudio_login2.png
copying images... [  4%] cyverse/../img/img_building_5.png
copying images... [  5%] docker/../img/dockerhub_create.png
copying images... [  6%] breakout/../img/jn_login2.png
copying images... [  7%] http://img.shields.io/badge/license-MIT-green.svg
copying images... [  8%] instructions_reporting/../img/static_site_docker.png
copying images... [  9%] cyverse/../img/img_building_8.png
copying images... [ 10%] cyverse/../img/img_building_9.png
copying images... [ 11%] docker/../img/dockerhub_autobuild.png
copying images... [ 12%] https://img.shields.io/pypi/v/pip.svg
copying images... [ 13%] cyverse/../img/atmo-1.1.png
copying images... [ 14%] cyverse/../img/cyverse_rgb.png
copying images... [ 15%] cyverse/../img/jupyter1-3.png
copying images... [ 16%] https://img.shields.io/travis/pypa/pip/master.svg
copying images... [ 17%] http://singularity.lbl.gov/assets/img/diagram/singularity-2.4-flow.png
copying images... [ 18%] breakout/../img/jn_login3.png
copying images... [ 19%] cyverse/../img/jupyter1-4.png
copying images... [ 20%] cyverse/../img/atmo-6.png
copying images... [ 21%] cyverse/../img/img_building_4.png
copying images... [ 22%] breakout/../img/rstudio_login.png
copying images... [ 23%] https://codecov.io/github/requests/requests/coverage.svg?branch=master
copying images... [ 24%] https://img.shields.io/pypi/v/urllib3.svg?maxAge=86400
copying images... [ 25%] getting_started/../img/cyverse_rgb.png
copying images... [ 26%] cyverse/../img/atmo-8.png
copying images... [ 27%] https://readthedocs.org/projects/pip/badge/?version=stable
copying images... [ 28%] cyverse/../img/atmo_launch0.png
copying images... [ 29%] https://readthedocs.org/projects/setuptools/badge/?version=latest
copying images... [ 30%] https://img.shields.io/appveyor/ci/pypa/pip.svg
copying images... [ 31%] cyverse/../img/auto-3.png
copying images... [ 32%] cyverse/../img/atmo_launch.png
copying images... [ 33%] docker/../img/pwd.png
copying images... [ 34%] https://badge.fury.io/py/idna.svg
copying images... [ 35%] cyverse/../img/auto-1.png
copying images... [ 36%] https://cloud.githubusercontent.com/assets/3028125/12213714/5b208976-b632-11e5-8406-38d379ec46aa.png
copying images... [ 37%] cyverse/../img/jupyter1-1.png
copying images... [ 38%] cyverse/../img/f1000.png
copying images... [ 39%] docker/../img/auto_build-6.png
copying images... [ 40%] https://travis-ci.org/shazow/urllib3.svg?branch=master
copying images... [ 41%] cyverse/../img/jupyter1-2.png
copying images... [ 42%] https://img.shields.io/coveralls/chardet/chardet/stable.svg
copying images... [ 43%] instructions_reporting/../img/instructors_code.png
copying images... [ 44%] https://img.shields.io/pypi/v/requests.svg
copying images... [ 45%] docker/../img/auto_build-7.png
copying images... [ 46%] docker/../img/portainer_demo.png
copying images... [ 47%] docker/../img/auto_build-5.png
copying images... [ 48%] cyverse/../img/jupyter1-7.png
copying images... [ 49%] cyverse/../img/atmo_cp.png
copying images... [ 50%] https://img.shields.io/codecov/c/github/shazow/urllib3.svg
copying images... [ 51%] https://readthedocs.org/projects/urllib3/badge/?version=latest
copying images... [ 52%] ./img/cc-main.png
copying images... [ 53%] docker/../img/bind_mount.png
copying images... [ 54%] docker/../img/create_repo2.png
copying images... [ 55%] docker/../img/volumes.png
copying images... [ 56%] https://img.shields.io/pypi/l/requests.svg
copying images... [ 57%] cyverse/../img/img_building_6.png
copying images... [ 58%] breakout/../img/rstudio_ss.png
copying images... [ 59%] https://img.shields.io/travis/pypa/setuptools/master.svg?label=Linux%20build%20%40%20Travis%20CI
copying images... [ 60%] cyverse/../img/auto-4.png
copying images... [ 61%] breakout/../img/snakemake.png
copying images... [ 62%] https://img.shields.io/pypi/v/setuptools.svg
copying images... [ 63%] cyverse/../img/atmo-9.png
copying images... [ 64%] cyverse/../img/jupyter1-6.png
copying images... [ 65%] http://img.shields.io/pypi/v/six.svg
copying images... [ 66%] cyverse/../img/img_building_1.png
copying images... [ 67%] https://travis-ci.org/benjaminp/six.svg?branch=master
copying images... [ 68%] https://img.shields.io/appveyor/ci/shazow/urllib3/master.svg
copying images... [ 69%] breakout/../img/jn_login.png
copying images... [ 70%] docker/../img/dockerhub_createrepo.png
copying images... [ 71%] cyverse/../img/jupyter1-8.png
copying images... [ 72%] cyverse/../img/jupyter1-9.png
copying images... [ 73%] https://img.shields.io/travis/chardet/chardet/stable.svg
copying images... [ 74%] docker/../img/private_registry.png
copying images... [ 75%] https://www.bountysource.com/badge/tracker?tracker_id=192525
copying images... [ 76%] docker/../img/dockerhub_autobuilds.png
copying images... [ 77%] docker/../img/docker.png
copying images... [ 78%] docker/../img/jn_galaxy.png
copying images... [ 79%] cyverse/../img/jupyter1-5.png
copying images... [ 80%] docker/../img/dockerhub_buildsettings.png
copying images... [ 81%] https://travis-ci.org/spinus/sphinxcontrib-images.svg?branch=master
copying images... [ 82%] cyverse/../img/atmo_launch1.png
copying images... [ 83%] docker/../img/dc-1.png
copying images... [ 84%] docker/../img/auto_build-2.1.png
copying images... [ 85%] docker/../img/docker_image.png
copying images... [ 86%] https://img.shields.io/github/contributors/requests/requests.svg
copying images... [ 87%] docker/../img/fastqe.png
copying images... [ 88%] cyverse/../img/img_building_3.png
copying images... [ 89%] docker/../img/jn_login.png
copying images... [ 90%] https://img.shields.io/pypi/v/chardet.svg
copying images... [ 91%] https://img.shields.io/pypi/pyversions/setuptools.svg
copying images... [ 92%] https://travis-ci.org/kjd/idna.svg?branch=master
copying images... [ 93%] docker/../img/create_repo.png
copying images... [ 94%] https://img.shields.io/pypi/pyversions/requests.svg
copying images... [ 95%] https://img.shields.io/appveyor/ci/jaraco/setuptools/master.svg?label=Windows%20build%20%40%20Appveyor
copying images... [ 96%] https://img.shields.io/pypi/l/chardet.svg
copying images... [ 97%] cyverse/../img/auto-2.png
copying images... [ 98%] breakout/../img/jn_login3.5.png
copying images... [100%] singularity/../img/singularity.png

copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/_static' does not exist
done
copying extra files... done
writing mimetype file...
writing META-INF/container.xml file...
writing content.opf file...
writing nav.xhtml file...
writing toc.ncx file...
writing CyVerseContainerCamp2019.epub file...
build succeeded, 65 warnings.

The ePub file is in _build/epub.

[rtd-command-info] start-time: 2019-07-17T18:02:39.385089Z, end-time: 2019-07-17T18:02:39.725154Z, duration: 0, exit-code: 0
mv -f /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/./_build/epub/CyVerseContainerCamp2019.epub /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/artifacts/latest/sphinx_epub/cyverse-container-camp-workshop-2019.epub