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 guide is intended to introduce new users to the Arvados system. It covers initial configuration required to access 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
+* Keep: Content-addressable cluster file system designed for robust storage of very large files, such as whole genome sequences running in the hundreds of gigabytes
+* Crunch: Cluster compute engine designed for genomic analysis, such as alignment and variant calls
+* Metadata Database: Information about the genomic data stored in Keep, such as genomic traits and human subjects
+* Workbench: Arvados' Web interface
h2. Prerequisites
To get the most value out of this guide, you should be comfortable with the following:
-# 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@
+# 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
+# Revision control using Git
-It will also be helpful (but not essential) if you are familiar with revision control using @git@.
+We also recommend you read the "Arvados Platform Overview":https://arvados.org/projects/arvados/wiki#Platform-Overview for an introduction and background information about Arvados.
-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 .
+The examples in this guide use the Arvados instance located at "https://{{ site.arvados_workbench_host }}/":https://{{ site.arvados_workbench_host }}/. 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.
-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.
+The Arvados public beta instance is located at "https://workbench.qr1hi.arvadosapi.com/":https://workbench.qr1hi.arvadosapi.com/. 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
<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">→</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">→</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
projects / arvados.git / blobdiff