Read the Docs build information
Build id: 190266
Project: cyverse-container-camp-workshop-2019
Version: latest
Commit: 7353116be2ac49bf5cc60ed4db87d7f29ee424a2
Date: 2019-03-08T14:03:55.591722Z
State: finished
Success: True
[rtd-command-info] start-time: 2019-03-08T14:03:56.134958Z, end-time: 2019-03-08T14:03:56.141795Z, 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: 2019-03-08T14:03:56.203468Z, end-time: 2019-03-08T14:03:57.205922Z, duration: 1, exit-code: 0
git fetch --tags --prune --prune-tags --depth 50
From https://github.com/CyVerse-learning-materials/container_camp_workshop_2019
ab17191..7353116 master -> origin/master
[rtd-command-info] start-time: 2019-03-08T14:03:57.367353Z, end-time: 2019-03-08T14:03:57.408315Z, duration: 0, exit-code: 0
git checkout --force origin/master
Previous HEAD position was ab17191 Update singularityadvanced.rst
HEAD is now at 7353116 Update agenda
[rtd-command-info] start-time: 2019-03-08T14:03:57.468902Z, end-time: 2019-03-08T14:03:57.506954Z, 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: 2019-03-08T14:03:58.186264Z, end-time: 2019-03-08T14:04:00.905741Z, duration: 2, 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: 2019-03-08T14:04:00.995868Z, end-time: 2019-03-08T14:04:01.605162Z, duration: 0, 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 (19.0.3)
[rtd-command-info] start-time: 2019-03-08T14:04:01.701685Z, end-time: 2019-03-08T14:04:03.872492Z, 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==2.2.0 setuptools<40 docutils==0.13.1 mock==1.0.1 pillow==2.6.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.5.4 recommonmark==0.4.0 sphinx<1.8 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<0.6
Requirement already up-to-date: Pygments==2.2.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (2.2.0)
Collecting setuptools<40
Using cached https://files.pythonhosted.org/packages/7f/e1/820d941153923aac1d49d7fc37e17b6e73bfbd2904959fffbad77900cf92/setuptools-39.2.0-py2.py3-none-any.whl
Requirement already up-to-date: docutils==0.13.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (0.13.1)
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==2.6.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (2.6.1)
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==0.5.4 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (0.5.4)
Requirement already up-to-date: recommonmark==0.4.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (0.4.0)
Requirement already up-to-date: sphinx<1.8 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/envs/latest/lib/python2.7/site-packages (1.7.9)
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: 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<1.8) (1.2.1)
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<1.8) (1.1.0)
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<1.8) (19.0)
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<1.8) (2.6.0)
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<1.8) (2.21.0)
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<1.8) (2.10)
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<1.8) (3.6.6)
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<1.8) (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<1.8) (1.12.0)
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<1.8) (2.3.1)
Requirement already satisfied, skipping upgrade: pytz>=0a 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<1.8) (2018.9)
Requirement already satisfied, skipping upgrade: urllib3<1.25,>=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<1.8) (1.24.1)
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<1.8) (2018.11.29)
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<1.8) (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<1.8) (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<1.8) (1.1.1)
Installing collected packages: setuptools
Found existing installation: setuptools 40.6.3
Uninstalling setuptools-40.6.3:
Successfully uninstalled setuptools-40.6.3
Successfully installed setuptools-39.2.0
[rtd-command-info] start-time: 2019-03-08T14:04:03.934980Z, end-time: 2019-03-08T14:04:04.463485Z, 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)) (1.7.9)
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)) (0.4.0)
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)) (0.6.5)
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)) (1.2.1)
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)) (2.2.0)
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)) (1.1.0)
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)) (2.6.0)
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)) (2.21.0)
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)) (39.2.0)
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: 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)) (0.13.1)
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)
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)) (3.6.6)
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<=0.5.4 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)) (0.5.4)
Requirement already satisfied: pytz>=0a 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)) (2018.9)
Requirement already satisfied: urllib3<1.25,>=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)) (1.24.1)
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)) (2018.11.29)
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: 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)) (2.3.1)
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)
[rtd-command-info] start-time: 2019-03-08T14:04:05.033060Z, end-time: 2019-03-08T14:04:05.093816Z, 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/"),
("htmlzip", "//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': '7353116b',
}
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"]
[rtd-command-info] start-time: 2019-03-08T14:04:05.165317Z, end-time: 2019-03-08T14:04:16.690162Z, duration: 11, exit-code: 0
python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
Running Sphinx v1.7.9
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
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**Biocontainers**
================
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.. currentmodule:: {{ module }}
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.. code-block:: bash
-v /home/username/your_data_folder:/data:ro
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$ docker inspect jupytertest
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**Workshop Code of Conduct and Other Information**
============================
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.. 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
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done
copying readthedocs static files... done
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dumping search index in English (code: en) ... done
dumping object inventory... done
build succeeded, 60 warnings.
The HTML pages are in _build/html.
[rtd-command-info] start-time: 2019-03-08T14:04:16.855848Z, end-time: 2019-03-08T14:04:18.984783Z, duration: 2, exit-code: 0
python sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia
Running Sphinx v1.7.9
loading translations [en]... done
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/home/docs/checkouts/readthedocs.org/user_builds/cyverse-container-camp-workshop-2019/checkouts/latest/singularity/singularityintro.rst:2: WARNING: Duplicate explicit target name: "singularity".
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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: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...
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copying readthedocs static files... done
copying extra files... done
dumping object inventory... done
build succeeded, 35 warnings.
The HTML page is in _build/localmedia.
[rtd-command-info] start-time: 2019-03-08T14:04:19.144224Z, end-time: 2019-03-08T14:04:22.059376Z, duration: 2, exit-code: 0
python sphinx-build -b latex -D language=en -d _build/doctrees . _build/latex
Running Sphinx v1.7.9
loading translations [en]... done
making output directory...
loading pickled environment... done
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building [latex]: all documents
updating environment: 0 added, 3 changed, 0 removed
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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
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Chapter 2.
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Chapter 13.
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Chapter 14.
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Chapter 15.
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Chapter 16.
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Chapter 18.
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Chapter 19.
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Chapter 20.
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Chapter 23.
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Chapter 24.
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[]|\T1/ptm/m/n/10 General in-tro-duc-tion to
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\T1/ptm/m/n/10 - Re-mote Pre-sen-ta-tion
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Chapter 4.
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Chapter 5.
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Chapter 6.
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Chapter 7.
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Chapter 8.
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Chapter 9.
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Chapter 10.
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Chapter 12.
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Chapter 13.
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Chapter 14.
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Chapter 15.
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Chapter 16.
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l.3396 ...your version of Linux/Windows/OSX/OS9
— well this is where D...
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l.3396 ...ersion of Linux/Windows/OSX/OS9 —
well this is where Docker ...
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Chapter 17.
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Chapter 18.
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Chapter 19.
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Chapter 20.
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Chapter 21.
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Chapter 22.
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Chapter 23.
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Chapter 24.
(./CyVerseDocumentation.ind) [131] (./CyVerseDocumentation.aux) )
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