X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/956093639196f92f3ad4b9e0795bcc7e30520e0d..759878e0a72644c5e537c51da9806672cf92e458:/doc/user/index.html.textile.liquid

diff --git a/doc/user/index.html.textile.liquid b/doc/user/index.html.textile.liquid
index 17c435ec35..46a55aec89 100644
--- a/doc/user/index.html.textile.liquid
+++ b/doc/user/index.html.textile.liquid
@@ -2,34 +2,20 @@
 layout: default
 navsection: userguide
 title: Welcome to Arvados!
-
 ...
 
-h1. Welcome to Arvados!
-
-This guide is intended to introduce new users to the Arvados system.  It covers initial configuration required to use the system and then presents several tutorials on using Arvados to do data processing.
-
-This user guide introduces how to use the major components of Arvados.  These are:
-
-* Keep: Content-addressable cluster file system designed for robust storage of very large files, such as whole genome sequences
-* Crunch: Cluster compute engine designed for genomic analysis, e.g. alignment, variant calls
-* Metadata Database: Information about the genomic data stored in Keep, such as genomic traits, human subjects
-* Workbench: Web interface to Arvados components
-
-h2. Prerequisites
+_If you are new to Arvados and want to get started quickly, go to "Accessing Arvados Workbench.":{{site.baseurl}}/user/getting_started/workbench.html_
 
-To get the most value out of this guide, you should be comfortable with the following:
+This guide provides an introduction to using Arvados to solve big data bioinformatics problems, including:
 
-# Using a secure shell client such as @ssh@ or @putty@ to log on to a remote server 
-# Using the unix command line shell @bash@
-# Viewing and editing files using a unix text editor such as @vi@, @emacs@, or @nano@
-# Programming in @python@
+* Robust storage of very large files, such as whole genome sequences, using the "Arvados Keep":{{site.baseurl}}/user/tutorials/tutorial-keep.html content-addressable cluster file system.
+* Running compute-intensive genomic analysis pipelines, such as alignment and variant calls using the "Arvados Crunch":{{site.baseurl}}/user/tutorials/intro-crunch.html cluster compute engine.
+* Storing and querying metadata about genome sequence files, such as human subjects and their phenotypic traits using the "Arvados Metadata Database.":{{site.baseurl}}/user/topics/tutorial-trait-search.html
+* Accessing, organizing, and sharing data, pipelines and results using the "Arvados Workbench":{{site.baseurl}}/user/getting_started/workbench.html web application.
 
-It will also be helpful (but not essential) if you are familiar with revision control using @git@.
+The examples in this guide use the Arvados instance located at <a href="https://{{ site.arvados_workbench_host }}/" target="_blank">https://{{ site.arvados_workbench_host }}</a>.  If you are using a different Arvados instance replace @{{ site.arvados_workbench_host }}@ with your private instance in all of the examples in this guide.
 
-The examples in this guide uses the public Arvados instance located at "https://workbench.{{ site.arvados_api_host }}/":https://workbench.{{ site.arvados_api_host }}/ .  You must have an account in order to use this service.  If you would like to request an account, please send an email to "arvados@curoverse.com":mailto:arvados@curoverse.com .
-
-If you are using a different Arvados instance replace @{{ site.arvados_api_host }}@ with your private instance in all of the examples in this guide.
+Curoverse maintains a public Arvados instance located at <a href="https://workbench.qr1hi.arvadosapi.com/" target="_blank">https://workbench.qr1hi.arvadosapi.com/</a>.  You must have an account in order to use this service.  If you would like to request an account, please send an email to "arvados@curoverse.com":mailto:arvados@curoverse.com.
 
 h2. Typographic conventions
 
@@ -37,15 +23,15 @@ This manual uses the following typographic conventions:
 
 <notextile>
 <ul>
-<li>Code blocks which are set aside from the text indicate user input to the system.  Commands that should be entered into a Unix shell are indicated with a '$' at the beginning of the line, and the entire user input <span class="userinput">will be highlighted</span>, possibly followed by example command output in black:
-<pre><code>$ <span class="userinput">ls foo</span>
-foo
-</code></pre></li>
+<li>Code blocks which are set aside from the text indicate user input to the system.  Commands that should be entered into a Unix shell are indicated by the directory where you should  enter the command ('~' indicates your home directory) followed by '$', followed by the highlighted <span class="userinput">command to enter</span> (do not enter the '$'), and possibly followed by example command output in black.  For example, the following block indicates that you should type <code>ls foo.*</code> while in your home directory and the expected output will be "foo.input" and "foo.output".
+<pre><code>~$ <span class="userinput">ls foo.*</span>
+foo.input foo.output
+</code></pre>
+</li>
+
 <li>Code blocks inline with text emphasize specific <code>programs</code>, <code>files</code>, or <code>options</code> that are being discussed.</li>
-<li>Bold text emphasizes <b>specific items</b> to look when discussing Arvados Workbench pages.</li>
-<li>A sequence of steps separated by right arrows (<span class="rarr">&rarr;</span>) indicate a path the user should follow through the Arvados Workbench to access some piece of information under discussion.  The steps indicate a menu, hyperlink, column name, field name, or other label on the page that guide the user where to look or click.
+<li>Bold text emphasizes <b>specific items</b> to review on Arvados Workbench pages.</li>
+<li>A sequence of steps separated by right arrows (<span class="rarr">&rarr;</span>) indicate a path the user should follow through the Arvados Workbench.  The steps indicate a menu, hyperlink, column name, field name, or other label on the page that guide the user where to look or click.
 </li>
 </ul>
 </notextile>
-
-Now begin by "accessing the Arvados workbench.":getting_started/workbench.html