QUICKSTART NAME¶

Goal¶

In this quick start you will learn how to foo.

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Section Name¶

Replace the text below with your own
Use the image src in this link to link to
- A DE App:
- An Atmosphere image:
Click Cancel to continue is how you can show a button
Tell the user to choose an appropriate value for a setting

sample-data

Tell them if they are following with our sample data exactly what value to choose

Summary¶

Next Steps:

Additional information, help¶

Fix or improve this documentation

Search for an answer: CyVerse Learning Center
Ask us for help: click on the lower right-hand side of the page
Report an issue or submit a change: Github Repo Link
Send feedback: learning@CyVerse.org

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STYLE TIPS - DELETE THIS PAGE BEFORE PUBLISHING¶

Tip

Check the code (.rst) source to see how these examples are written in restructured text.

Many of the examples Writing your documentation using sample data¶

Where possible, you want write documentation instructions to be general enough for users can follow along with their own data. To help do this, you can use the sample data admonition to intersperse sample data-specific instructions into your generic instructions.

To do this, start your documentation with a description and where possible, a citation of the data:

Sample data

How to use provided sample data

In this guide, we will use an RNA-Seq dataset (“Zika infected hNPCs”). This experiment compared human neuroprogenetor cells (hNPCs) infected with the Zika virus to non-infected hNPCs. You can read more about the experimental conditions and methods here. Where appropriate, a note (in this orange colored background) in the instructions will indicate which options to select to make use of this provided dataset.

Sample data citation: Yi L, Pimentel H, Pachter L (2017) Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways. PLOS ONE 12(4): e0175744. 10.1371/journal.pone.0175744

Then, as you have instructions, intersperse the sample data .. admonition

First, enter the cutoff value for your dataset

Sample data

“Zika infected hNPCs” dataset:

Enter 30

Continue with next step…

Other admonitions¶

There are several admonitions you can use, but tip and warning are the most common for our documentation.

Tip

If you don’t see a desired species/genome contact us to have it added

Warning

When naming your samples and conditions, avoid spaces and special characters (e.g. !#$%^&/, etc.). Also be sure to be consistent with spelling.

Buttons and keyboard combinations¶

Where it adds clarity you can use this text to add buttons:

Click Cancel to continue

Press Control + P to print your result

Fix the link in custom_url.txt to use this button to launch a quicklaunch link in the DE (the embed HTML the DE generates may not render properly in RTD)

Detail expand questions¶

You can have questions by using .. admonition:: Question and .. admonition:: Answer. Just make sure you pay attention to spacing as below.

Question

Test your reader’s knowledge with a question

Answer

Give them an answer

Test your reader’s knowledge with a question

Answer

Give them an answer

Embed video¶

You can embed responsive YouTube videos:

URLs/Links¶

Have hyperlinks open in a new tab to avoid pushing the reader off the documentation page. Always use substitutions. Best practice is to define your substitutions in the cyverse_rst_defined_substitutions.txt file in this repo for easy future updating.

Bad link …

bad google

Good link …

Google

Even better link (because it is defined in a separate file)

CyVerse User Portal

Images¶

Images should only be used when necessary.

Choose an image size that works for your page:

Better size:

Images should have a 1px black border:

Quick Start Maintainer(s)¶

Who to contact if this quick start needs fixing. You can also email learning@CyVerse.org

Maintainer	Institution	Contact
Your Name	CyVerse / UA	Yourname@email.com

Prerequisites¶

Downloads, access, and services¶

In order to complete this tutorial you will need access to the following services/software

Prerequisite Preparation/Notes Link/Download

CyVerse account You will need a CyVerse account to complete this exercise CyVerse User Portal

Atmosphere access You must have access to Atmosphere CyVerse User Portal

Cyberduck Standalone software for upload/download to Data Store Download Cyberduck

Platform(s)¶

We will use the following CyVerse platform(s):

Input and example data¶

In order to complete this quickstart you will need to have the following inputs prepared

Input File(s)	Format	Preparation/Notes	Example Data

Get Started¶

Replace the text below with your own
Use the image src in this link to link to
- A DE App:
- An Atmosphere image:
Click Cancel to continue is how you can show a button
Tell the user to choose an appropriate value for a setting

sample-data

Tell them if they are following with our sample data exactly what value to choose

Summary¶

Next Steps:

Some common next steps include:

Step
Step

Additional information, help¶

Fix or improve this documentation

Search for an answer: CyVerse Learning Center
Ask us for help: click on the lower right-hand side of the page
Report an issue or submit a change: Github Repo Link
Send feedback: learning@CyVerse.org

Learning Center Home