[ARVADOS] created: 88be56a262ab073e6aa96bdf6f80464731562a33
git at public.curoverse.com
git at public.curoverse.com
Wed Oct 14 15:01:15 EDT 2015
at 88be56a262ab073e6aa96bdf6f80464731562a33 (commit)
commit 88be56a262ab073e6aa96bdf6f80464731562a33
Author: Bryan Cosca <bcosc at curoverse.com>
Date: Wed Oct 14 15:01:00 2015 -0400
7015: Tested up to Accessing an Arvados VM with Webshell
diff --git a/doc/index.html.liquid b/doc/index.html.liquid
index 8cbf959..31a86c2 100644
--- a/doc/index.html.liquid
+++ b/doc/index.html.liquid
@@ -41,7 +41,7 @@ title: Arvados | Documentation
<div class="col-sm-6" style="border-left: solid; border-width: 1px">
<p><strong>Quickstart</strong>
<p>
- Try any pipeline from the <a href="https://dev.arvados.org/projects/arvados/wiki/Public_Pipelines_and_Datasets">list of public pipelines</a>. For instance, the <a href="http://curover.se/pathomap">Pathomap Pipeline</a> links to these <a href="https://dev.arvados.org/projects/arvados/wiki/pathomap_tutorial/">step-by-step instructions</a> for trying Arvados out right in your browser using Curoverse's <a href="http://lp.curoverse.com/beta-signup/">public Arvados instance</a>.
+ Try any pipeline from the <a href="https://cloud.curoverse.com/projects/public">list of public pipelines</a>. For instance, the <a href="http://curover.se/pathomap">Pathomap Pipeline</a> links to these <a href="https://dev.arvados.org/projects/arvados/wiki/pathomap_tutorial/">step-by-step instructions</a> for trying Arvados out right in your browser using Curoverse's <a href="http://lp.curoverse.com/beta-signup/">public Arvados instance</a>.
</p>
<!--<p>-->
<!--<ol>-->
diff --git a/doc/user/getting_started/ssh-access-unix.html.textile.liquid b/doc/user/getting_started/ssh-access-unix.html.textile.liquid
index a9eb8c1..e4f37ec 100644
--- a/doc/user/getting_started/ssh-access-unix.html.textile.liquid
+++ b/doc/user/getting_started/ssh-access-unix.html.textile.liquid
@@ -4,7 +4,7 @@ navsection: userguide
title: Accessing an Arvados VM with SSH - Unix Environments
...
-This document is for accessing an arvados VM using SSK keys in Unix environments (Linux, OS X, Cygwin). If you would like to access VM through your browser, please visit the "Accessing an Arvados VM with Webshell":vm-login-with-webshell.html page. If you are using a Windows environment, please visit the "Accessing an Arvados VM with SSH - Windows Environments":ssh-access-windows.html page.
+This document is for accessing an arvados VM using SSH keys in Unix environments (Linux, OS X, Cygwin). If you would like to access VM through your browser, please visit the "Accessing an Arvados VM with Webshell":vm-login-with-webshell.html page. If you are using a Windows environment, please visit the "Accessing an Arvados VM with SSH - Windows Environments":ssh-access-windows.html page.
{% include 'ssh_intro' %}
diff --git a/doc/user/getting_started/vm-login-with-webshell.html.textile.liquid b/doc/user/getting_started/vm-login-with-webshell.html.textile.liquid
index 50fa474..58ad868 100644
--- a/doc/user/getting_started/vm-login-with-webshell.html.textile.liquid
+++ b/doc/user/getting_started/vm-login-with-webshell.html.textile.liquid
@@ -10,7 +10,7 @@ h2(#webshell). Access VM using webshell
Webshell gives you access to an arvados virtual machine from your browser with no additional setup.
-In the Arvados Workbench, click on the dropdown menu icon <span class="fa fa-lg fa-user"></span> <span class="caret"></span> in the upper right corner of the top navigation menu to access the user settings menu, and click on the menu item *Virtual machines* to see the list of virtual machines you can access.
+In the Arvados Workbench, click on the dropdown menu icon <span class="fa fa-lg fa-user"></span> <span class="caret"></span> in the upper right corner of the top navigation menu to access the user settings menu, and click on the menu item *Virtual machines* to see the list of virtual machines you can access. If you do not have access to any virtual machines, please click on <span class="btn btn-sm btn-primary">Send request for shell access</span> or send an email to "support at curoverse.com":mailto:support at curoverse.com.
Each row in the Virtual Machines panel lists the hostname of the VM, along with a <code>Log in as *you*</code> button under the column "Web shell beta". Clicking on this button will open up a webshell terminal for you in a new browser tab and log you in.
diff --git a/doc/user/index.html.textile.liquid b/doc/user/index.html.textile.liquid
index 0967cbc..636dce0 100644
--- a/doc/user/index.html.textile.liquid
+++ b/doc/user/index.html.textile.liquid
@@ -13,9 +13,7 @@ This guide provides a reference for using Arvados to solve big data bioinformati
* 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.
-The examples in this guide use the Arvados instance located at <a href="{{site.arvados_workbench_host}}/" target="_blank">{{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.
-
-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 at curoverse.com":mailto:arvados at curoverse.com.
+The examples in this guide use the public Arvados instance located at <a href="{{site.arvados_workbench_host}}/" target="_blank">{{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.
h2. Typographic conventions
diff --git a/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid b/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid
index f9522fb..fac573a 100644
--- a/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid
@@ -18,13 +18,13 @@ h3. Steps
# Start from the *Workbench Dashboard*. You can access the Dashboard by clicking on *<i class="fa fa-lg fa-fw fa-dashboard"></i> Dashboard* in the upper left corner of any Workbench page.
# Click on the <span class="btn btn-sm btn-primary"><i class="fa fa-fw fa-gear"></i> Run a pipeline...</span> button. This will open a dialog box titled *Choose a pipeline to run*.
-# Click to open the *All projects <span class="caret"></span>* menu. Under the *Projects shared with me* header, select *<i class="fa fa-fw fa-share-alt"></i> Arvados Tutorial*.
+# In the search box, type in *Tutorial align using bwa mem*.
# Select *<i class="fa fa-fw fa-gear"></i> Tutorial align using bwa mem* and click the <span class="btn btn-sm btn-primary" >Next: choose inputs <i class="fa fa-fw fa-arrow-circle-right"></i></span> button. This will create a new pipeline in your *Home* project and will open it. You can now supply the inputs for the pipeline.
# The first input parameter to the pipeline is *"reference_collection" parameter for run-command script in bwa-mem component*. Click the <span class="btn btn-sm btn-primary">Choose</span> button beneath that header. This will open a dialog box titled *Choose a dataset for "reference_collection" parameter for run-command script in bwa-mem component*.
-# Once again, open the *All projects <span class="caret"></span>* menu and select *<i class="fa fa-fw fa-share-alt"></i> Arvados Tutorial*. Select *<i class="fa fa-fw fa-archive"></i> Tutorial chromosome 19 reference* and click the <span class="btn btn-sm btn-primary" >OK</span> button.
+# Open the *Home <span class="caret"></span>* menu and select *All Projects*. Search for and select *<i class="fa fa-fw fa-archive"></i> Tutorial chromosome 19 reference* and click the <span class="btn btn-sm btn-primary" >OK</span> button.
# Repeat the previous two steps to set the *"sample" parameter for run-command script in bwa-mem component* parameter to *<i class="fa fa-fw fa-archive"></i> Tutorial sample exome*.
# Click on the <span class="btn btn-sm btn-primary" >Run <i class="fa fa-fw fa-play"></i></span> button. The page updates to show you that the pipeline has been submitted to run on the Arvados cluster.
-# After the pipeline starts running, you can track the progress by watching log messages from jobs. This page refreshes automatically. You will see a <span class="label label-success">complete</span> label under the *job* column when the pipeline completes successfully.
+# After the pipeline starts running, you can track the progress by watching log messages from jobs. This page refreshes automatically. You will see a <span class="label label-success">complete</span> label when the pipeline completes successfully.
# Click on the *Output* link to see the results of the job. This will load a new page listing the output files from this pipeline. You'll see the output SAM file from the alignment tool under the *Files* tab.
# Click on the <span class="btn btn-sm btn-info"><i class="fa fa-download"></i></span> download button to the right of the SAM file to download your results.
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