Read the Docs build information
Build id: 257144
Project: cyverse-learning-materials-home
Version: latest
Commit: 113dfac1c1e111a0820ee5e5617f366c89331ccf
Date: 2019-11-06T21:13:16.274825Z
State: finished
Success: True


[rtd-command-info] start-time: 2019-11-06T21:13:17.102735Z, end-time: 2019-11-06T21:13:17.115803Z, duration: 0, exit-code: 0
git remote set-url origin https://github.com/CyVerse-learning-materials/learning-materials-home.git


[rtd-command-info] start-time: 2019-11-06T21:13:17.297921Z, end-time: 2019-11-06T21:13:17.758737Z, duration: 0, exit-code: 0
git fetch origin --force --tags --prune --prune-tags --depth 50
From https://github.com/CyVerse-learning-materials/learning-materials-home
   2009654..113dfac  master     -> origin/master

[rtd-command-info] start-time: 2019-11-06T21:13:17.970081Z, end-time: 2019-11-06T21:13:17.983755Z, duration: 0, exit-code: 0
git checkout --force origin/master
Previous HEAD position was 2009654 Update webinars.rst
HEAD is now at 113dfac Update tutorials.rst

[rtd-command-info] start-time: 2019-11-06T21:13:18.065347Z, end-time: 2019-11-06T21:13:18.086602Z, duration: 0, exit-code: 0
git clean -d -f -f
Removing _build/
Removing misc/__init__.pyc
Removing misc/cyverse_sphinx_conf.pyc

[rtd-command-info] start-time: 2019-11-06T21:13:19.133801Z, end-time: 2019-11-06T21:13:22.717232Z, 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-learning-materials-home/envs/latest/bin/python2.7
Not overwriting existing python script /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/bin/python (you must use /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/bin/python2.7)
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2019-11-06T21:13:22.821501Z, end-time: 2019-11-06T21:13:23.687219Z, duration: 0, exit-code: 0
python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/.cache/pip pip
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7.
Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/lib/python2.7/site-packages (19.3.1)

[rtd-command-info] start-time: 2019-11-06T21:13:23.765779Z, end-time: 2019-11-06T21:13:25.903968Z, duration: 2, exit-code: 0
python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/.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<1.1
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7.
Requirement already up-to-date: Pygments==2.3.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/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-learning-materials-home/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-learning-materials-home/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-learning-materials-home/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-learning-materials-home/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-learning-materials-home/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-learning-materials-home/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-learning-materials-home/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-learning-materials-home/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-learning-materials-home/envs/latest/lib/python2.7/site-packages (0.4.3)
Requirement already up-to-date: readthedocs-sphinx-ext<1.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/lib/python2.7/site-packages (1.0.0)
Requirement already satisfied, skipping upgrade: future in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/lib/python2.7/site-packages (from commonmark==0.8.1) (0.18.2)
Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/lib/python2.7/site-packages (from sphinx<2) (2.0.0)
Requirement already satisfied, skipping upgrade: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/lib/python2.7/site-packages (from sphinx<2) (1.1.2)
Requirement already satisfied, skipping upgrade: packaging in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/lib/python2.7/site-packages (from sphinx<2) (19.2)
Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/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-learning-materials-home/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-learning-materials-home/envs/latest/lib/python2.7/site-packages (from sphinx<2) (2.10.3)
Requirement already satisfied, skipping upgrade: typing; python_version < "3.5" in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/lib/python2.7/site-packages (from sphinx<2) (3.7.4.1)
Requirement already satisfied, skipping upgrade: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/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-learning-materials-home/envs/latest/lib/python2.7/site-packages (from sphinx<2) (1.13.0)
Requirement already satisfied, skipping upgrade: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/lib/python2.7/site-packages (from packaging->sphinx<2) (2.4.4)
Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/lib/python2.7/site-packages (from babel!=2.0,>=1.3->sphinx<2) (2019.3)
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-learning-materials-home/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx<2) (1.25.6)
Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx<2) (2019.9.11)
Requirement already satisfied, skipping upgrade: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/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-learning-materials-home/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-learning-materials-home/envs/latest/lib/python2.7/site-packages (from Jinja2>=2.3->sphinx<2) (1.1.1)

[rtd-command-info] start-time: 2019-11-06T21:13:27.981256Z, end-time: 2019-11-06T21:13:28.291056Z, 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 Learning Center Home'
copyright = '2019, CyVerse'
author = 'CyVerse'
version = '0.1b.0'
release = '0.1b.0'

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

# html theme configuration -- see https://sphinx-rtd-theme.readthedocs.io/en/stable/configuring.html

html_theme_options = {
# Table of Content options
    'collapse_navigation': True,
    'sticky_navigation': True,
    'navigation_depth': 4,
    'includehidden': True,
    'titles_only': False
}




###########################################################################
#          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 multiple suffixes
        SUFFIX = list(source_suffix.keys())[0]  # make a ``list()`` for py2/py3 compatibility
    else:
        # default to .rst
        SUFFIX = '.rst'
else:
    SUFFIX = '.rst'

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

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

if globals().get('websupport2_base_url', False):
    websupport2_base_url = 'https://readthedocs.com/websupport'
    websupport2_static_url = 'https://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': [ 
    ("html", "//readthedocs.com/projects/cyverse-learning-materials-home/downloads/htmlzip/latest/"),
    ],
    'subprojects': [ 
        ("cyverse-discovery-environment-guide", "https://learning.cyverse.org/projects/discovery-environment-guide/en/latest/"),
        ("cyverse-atmosphere-guide", "https://learning.cyverse.org/projects/atmosphere-guide/en/latest/"),
        ("cyverse-account-creation-quickstart", "https://learning.cyverse.org/projects/cyverse-account-creation-quickstart/en/latest/"),
        ("cyverse-importing-sradata-quickstart", "https://learning.cyverse.org/projects/cyverse-importing-sradata-quickstart/en/latest/"),
        ("cyverse-dnasubway-guide", "https://learning.cyverse.org/projects/dnasubway_guide/en/latest/"),
        ("cyverse-trimmomatic-quickstart", "https://learning.cyverse.org/projects/trimmomatic_quickstart/en/latest/"),
        ("cyverse-data-store-guide", "https://learning.cyverse.org/projects/data_store_guide/en/latest/"),
        ("cyverse-fastqc-quickstart", "https://learning.cyverse.org/projects/fastqc_quickstart/en/latest/"),
        ("cyverse-kallisto-tutorial", "https://learning.cyverse.org/projects/kallisto_tutorial/en/latest/"),
        ("cyverse-sra-submission-quickstart", "https://learning.cyverse.org/projects/sra_submission_quickstart/en/latest/"),
        ("cyverse-sciapps-guide", "https://learning.cyverse.org/projects/SciApps Guide/en/latest/"),
        ("cyverse-documentation-quickstart", "https://learning.cyverse.org/projects/Documentation-Quickstart/en/latest/"),
        ("cyverse-group-project-quickstart", "https://learning.cyverse.org/projects/cyverse-group-project-quickstart/en/latest/"),
        ("cyverse-container-camp-workshop-2019", "https://learning.cyverse.org/projects/container_camp_workshop_2019/en/latest/"),
        ("cyverse-creating-docker-containers-quickstart", "https://learning.cyverse.org/projects/cyverse-creating-docker-containers-quickstart/en/latest/"),
        ("cyverse-learning-center-faq", "https://learning.cyverse.org/projects/faq/en/latest/"),
        ("cyverse-240-minute-r-tutorial", "https://learning.cyverse.org/projects/cyverse-240-minute-r-tutorial/en/latest/"),
        ("cyverse-git-for-mere-mortals", "https://learning.cyverse.org/projects/cyverse-git-for-mere-mortals/en/latest/"),
        ("cyverse-cyverse-tools-and-services-workshop", "https://learning.cyverse.org/projects/cyverse-cyverse-tools-and-services-workshop/en/latest/"),
        ("cyverse-visual-interactive-computing-environment", "https://learning.cyverse.org/projects/vice/en/latest/"),
        ("cyverse-doi-request-quickstart", "https://learning.cyverse.org/projects/cyverse-doi-request-quickstart/en/latest/"),
        ("cyverse-foundational-open-science-skills-2020", "https://learning.cyverse.org/projects/foss-2020/en/latest/"),
    ],
    'slug': 'cyverse-learning-materials-home',
    'name': u'learning-materials-home',
    'rtd_language': u'en',
    'programming_language': u'words',
    'canonical_url': 'https://learning.cyverse.org/en/latest/',
    'analytics_code': '',
    'single_version': False,
    'conf_py_path': '/',
    'api_host': 'https://readthedocs.com',
    'github_user': 'CyVerse-learning-materials',
    'github_repo': 'learning-materials-home',
    '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': '113dfac1',
}




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

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

# Add External version warning banner to the external version documentation
if 'branch' == 'external':
    extensions.insert(1, "readthedocs_ext.external_version_warning")

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: 2019-11-06T21:13:28.393424Z, end-time: 2019-11-06T21:13:30.678824Z, duration: 2, 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 10 source files that are out of date
updating environment: 10 added, 0 changed, 0 removed
reading sources... [ 10%] README
reading sources... [ 20%] contributing
reading sources... [ 30%] index
reading sources... [ 40%] platform_guides
reading sources... [ 50%] power_users
reading sources... [ 60%] quick_starts
reading sources... [ 70%] tools_and_apps
reading sources... [ 80%] tutorials
reading sources... [ 90%] webinars
reading sources... [100%] workshops

/home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/README.rst:21: WARNING: Duplicate explicit target name: "tutorials@cyverse.org".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/README.rst:170: WARNING: Duplicate substitution definition name: "Powered by CyVerse".
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README.rst:21: WARNING: Duplicate explicit target name: "tutorials@cyverse.org".
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/home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/platform_guides.rst:100: WARNING: Duplicate substitution definition name: "Github Repo Link".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/power_users.rst:36: WARNING: Undefined substitution referenced: "External Collaborative Partnership".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/power_users.rst:36: WARNING: Undefined substitution referenced: "ECP Request web form".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/quick_starts.rst:125: WARNING: Duplicate substitution definition name: "Data Store".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/tools_and_apps.rst:11: WARNING: Title underline too short.

Tool and App Integration
-----------
cyverse_rst_defined_substitutions.txt:32: WARNING: Document may not end with a transition.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/tutorials.rst:74: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/tutorials.rst:79: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/tutorials.rst:67: WARNING: Error parsing content block for the "list-table" directive: two-level bullet list expected, but row 2 does not contain a second-level bullet list.

.. list-table::
    :header-rows: 1

    * - Tutorial
      - Notes
    * - |Basic Stacks|
      - Use next generation sequence data produced from Reduced Representation Libraries (RRL) such as
      Restriction site associated (RAD) tags.
    * - |BATools 0.0.1|
      - Introduce new users to BATools and the BATools Wrapper Script.
    * - |Evolinc|
      - Evolinc is a two-part pipeline to identify lincRNAs from an assembled transcriptome file (.gtf output
      from cufflinks) and then determine the extent to which those lincRNAs are conserved in the genome and
      transcriptome of other species.
    * - |FaST-LMM.Py v2.02|
      - Introduce new users to the FaST-LMM software for GWAS analysis.
    * - |fastStructure|
      - fastStructure is a fast algorithm for inferring population structure from large SNP genotype data. It is based on a variational Bayesian framework for posterior inference and is written in Python2.x.
    * - |Installing R packages on Atmosphere|
      - Install R packages on Atmosphere: Launch instance, transfer files to instance, install R package, request imaging.
    * - |KOBAS 2.0-09052014|
      - Learn how to annotate and identify using KOBAS 2.0.
    * - |QIIME-1.9.1 for Atmosphere|
      - QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data. QIIME is designed to take users from raw sequencing data generated on the Illumina or other platforms through publication quality graphics and statistics. QIIME has been applied to studies based on billions of sequences from tens of thousands of samples.
    * - |QUAST 4.0|
      - QUAST is a tool for  evaluating genome assemblies by computing various metrics.
    * - |rnaQUAST 1.1.0|
      - rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference genome and gene data database. In addition, rnaQUAST is also capable of estimating gene database coverage by raw reads and de novo quality assessment using third-party software (STAR, TopHat, GMAP etc.).
    * - |rnaQUAST 1.2.0|
      - rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference genome and gene data database. In addition, rnaQUAST is also capable of estimating gene database coverage by raw reads and de novo quality assessment using third-party software (STAR, TopHat, GMAP etc.).
    * - |Validate Workflow v0.9|
      - Learn to navigate the Validate Workflow.
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Tool and App Integration
-----------
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.. list-table::
    :header-rows: 1

    * - Tutorial
      - Notes
    * - |Basic Stacks|
      - Use next generation sequence data produced from Reduced Representation Libraries (RRL) such as
      Restriction site associated (RAD) tags.
    * - |BATools 0.0.1|
      - Introduce new users to BATools and the BATools Wrapper Script.
    * - |Evolinc|
      - Evolinc is a two-part pipeline to identify lincRNAs from an assembled transcriptome file (.gtf output
      from cufflinks) and then determine the extent to which those lincRNAs are conserved in the genome and
      transcriptome of other species.
    * - |FaST-LMM.Py v2.02|
      - Introduce new users to the FaST-LMM software for GWAS analysis.
    * - |fastStructure|
      - fastStructure is a fast algorithm for inferring population structure from large SNP genotype data. It is based on a variational Bayesian framework for posterior inference and is written in Python2.x.
    * - |Installing R packages on Atmosphere|
      - Install R packages on Atmosphere: Launch instance, transfer files to instance, install R package, request imaging.
    * - |KOBAS 2.0-09052014|
      - Learn how to annotate and identify using KOBAS 2.0.
    * - |QIIME-1.9.1 for Atmosphere|
      - QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data. QIIME is designed to take users from raw sequencing data generated on the Illumina or other platforms through publication quality graphics and statistics. QIIME has been applied to studies based on billions of sequences from tens of thousands of samples.
    * - |QUAST 4.0|
      - QUAST is a tool for  evaluating genome assemblies by computing various metrics.
    * - |rnaQUAST 1.1.0|
      - rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference genome and gene data database. In addition, rnaQUAST is also capable of estimating gene database coverage by raw reads and de novo quality assessment using third-party software (STAR, TopHat, GMAP etc.).
    * - |rnaQUAST 1.2.0|
      - rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference genome and gene data database. In addition, rnaQUAST is also capable of estimating gene database coverage by raw reads and de novo quality assessment using third-party software (STAR, TopHat, GMAP etc.).
    * - |Validate Workflow v0.9|
      - Learn to navigate the Validate Workflow.
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