[ARVADOS] updated: 8a2a84af560d9de68cf0d0c9e34e0d1f19b65e43
git at public.curoverse.com
git at public.curoverse.com
Mon May 25 18:45:10 EDT 2015
Summary of changes:
doc/_includes/_ssh_addkey.liquid | 9 ++++++---
doc/index.html.liquid | 5 ++---
doc/user/getting_started/community.html.textile.liquid | 4 ++--
.../tutorials/tutorial-pipeline-workbench.html.textile.liquid | 8 +++++---
4 files changed, 15 insertions(+), 11 deletions(-)
via 8a2a84af560d9de68cf0d0c9e34e0d1f19b65e43 (commit)
from 0f125dd51c7dc13047672dee5362866f31885e0a (commit)
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commit 8a2a84af560d9de68cf0d0c9e34e0d1f19b65e43
Author: radhika <radhika at curoverse.com>
Date: Mon May 25 18:36:49 2015 -0400
6093: doc updates
diff --git a/doc/_includes/_ssh_addkey.liquid b/doc/_includes/_ssh_addkey.liquid
index 3770635..08d699e 100644
--- a/doc/_includes/_ssh_addkey.liquid
+++ b/doc/_includes/_ssh_addkey.liquid
@@ -5,11 +5,14 @@ h1(#workbench). Adding your key to Arvados Workbench
h3. From the Workbench dashboard
-If you have no SSH keys registered, there should be a notification asking you to provide your SSH public key. In the Workbench top navigation menu, look for a dropdown menu with your email address in upper right corner. It will have an icon such as <span class="badge badge-alert">1</span> (the number indicates there are new notifications). Click on this icon and a dropdown menu should appear with a message asking you to add your public key. Paste your public key into the text area provided and click on the check button to submit the key. You are now ready to "log into an Arvados VM":#login.
+If you have no SSH keys registered, there should be a notification asking you to provide your SSH public key. In the Workbench top navigation menu, look for a dropdown menu with an icon such as <span class="badge badge-alert">1</span> <span class="fa fa-lg fa-user"></span> <span class="caret"></span> (the number indicates there are new notifications). Click on this icon and a dropdown menu should appear with a message asking you to add your public key. Click on the link *Click here to set up an SSH public key for use with Arvados*. This will take you to the *Manage account* page. Click on the <span class="btn btn-primary">*+* Add new SSH key</span> button in this page. This will open a popup as shown in this screenshot:
+
+!{{ site.baseurl }}/images/ssh-adding-public-key.png!
+Paste your public key into the text area labeled *Public Key*, and click on the <span class="btn btn-primary">Submit</span> button. You are now ready to "log into an Arvados VM":#login.
h3. Alternate way to add SSH keys
-Click on the link with your _email address_ in the upper right corner to access the user settings menu, and click on the menu item *Manage account* to go to the account management page.
+Click on the dropdown menu icon <span class="badge badge-alert">1</span> <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 *Manage account* to go to the account management page.
On the *Manage account* page, click on the button <span class="btn btn-primary">*+* Add new SSH key</span> button in the upper right corner of the page in the SSH Keys panel.
@@ -21,6 +24,6 @@ Paste the public key that you copied to the cliboard in the previous section int
h1(#login). Using SSH to log into an Arvados VM
-To see a list of virtual machines that you have access to and determine the name and login information, click on the link with your _email address_ in the upper right corner and click on the menu item *Manage account* to go to the account management page. On this page, you will see a *Virtual Machines* panel, which lists the virtual machines you can access. The *hostname* column lists the name of each available VM. The *logins* column will have a list of comma separated values of the form @you at . In this guide the hostname will be *_shell_* and the login will be *_you_*. Replace these with your hostname and login name as appropriate.
+To see a list of virtual machines that you have access to and determine the name and login information, 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 *Manage account* to go to the account management page. On this page, you will see a *Virtual Machines* panel, which lists the virtual machines you can access. The *hostname* column lists the name of each available VM. The *logins* column will have a list of comma separated values of the form @you at . In this guide the hostname will be *_shell_* and the login will be *_you_*. Replace these with your hostname and login name as appropriate.
diff --git a/doc/index.html.liquid b/doc/index.html.liquid
index 4e951d6..35cf704 100644
--- a/doc/index.html.liquid
+++ b/doc/index.html.liquid
@@ -25,11 +25,10 @@ title: Arvados | Documentation
<p><strong>What is Arvados</strong>
<p><a href="https://arvados.org/">Arvados</a> enables you to quickly begin using cloud computing resources in your data science work. It allows you to track your methods and datasets, share them securely, and easily re-run analyses.
</p>
- <p><strong>News</strong>
+ <p><strong>Communications</strong>
<p>Read our <a href="https://arvados.org/projects/arvados/blogs">blog updates</a> or look through our <a href="https://arvados.org/projects/arvados/activity">recent developer activity</a>.
</p>
- <p><strong>Questions?</strong></p>
- <p>Email <a href="http://lists.arvados.org/mailman/listinfo/arvados">the mailing list</a>, or chat with us on IRC: <a href="irc://irc.oftc.net:6667/#arvados">#arvados</a> @ OFTC (you can <a href="https://webchat.oftc.net/?channels=arvados">join in your browser</a>).
+ <p>Questions? Email <a href="http://lists.arvados.org/mailman/listinfo/arvados">the mailing list</a>, or chat with us on IRC: <a href="irc://irc.oftc.net:6667/#arvados">#arvados</a> @ OFTC (you can <a href="https://webchat.oftc.net/?channels=arvados">join in your browser</a>).
</p>
<p><strong>Want to contribute?</strong></p>
<p>Check out our <a href="https://arvados.org/projects/arvados">developer site</a>. We're open source, check out our code on <a href="https://github.com/curoverse/arvados">github</a>.
diff --git a/doc/user/getting_started/community.html.textile.liquid b/doc/user/getting_started/community.html.textile.liquid
index 8b6e22d..7ef903c 100644
--- a/doc/user/getting_started/community.html.textile.liquid
+++ b/doc/user/getting_started/community.html.textile.liquid
@@ -6,7 +6,7 @@ title: Arvados Community and Getting Help
h2. On the web
-The Arvados Free Sofware project page is located at "http://arvados.org":http://arvados.org . The "Arvados Wiki":https://arvados.org/projects/arvados/wiki is a collaborative site for documenting Arvados has an overview of the Arvados Platform and Components. The "Arvados blog":https://arvados.org/projects/arvados/blogs posts articles of interest about Arvados.
+The Arvados Free Sofware project page is located at "http://arvados.org":http://arvados.org . The "Arvados Wiki":https://arvados.org/projects/arvados/wiki is a collaborative site for documenting Arvados and provides an overview of the Arvados Platform and Components. The "Arvados blog":https://arvados.org/projects/arvados/blogs posts articles of interest about Arvados.
h2. Mailing lists
@@ -14,7 +14,7 @@ The "Arvados user mailing list":http://lists.arvados.org/mailman/listinfo/arvado
h2. IRC
-The "#arvados":irc://irc.oftc.net:6667/#arvados IRC (Internet Relay Chat) channel at on the "Open and Free Technology Community (irc.oftc.net)":http://www.oftc.net/oftc/ is available for live discussion and support. You can use a traditional IRC client or "join OFTC over the web.":https://webchat.oftc.net/?channels=arvados
+The "#arvados":irc://irc.oftc.net:6667/#arvados IRC (Internet Relay Chat) channel at the "Open and Free Technology Community (irc.oftc.net)":http://www.oftc.net/oftc/ is available for live discussion and support. You can use a traditional IRC client or "join OFTC over the web.":https://webchat.oftc.net/?channels=arvados
h2. Bug tracking
diff --git a/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid b/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid
index 8dad6ab..f9522fb 100644
--- a/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid
@@ -6,7 +6,7 @@ title: "Running a pipeline using Workbench"
A "pipeline" (sometimes called a "workflow" in other systems) is a sequence of steps that apply various programs or tools to transform input data to output data. Pipelines are the principal means of performing computation with Arvados. This tutorial demonstrates how to run a single-stage pipeline to take a small data set of paired-end reads from a sample "exome":https://en.wikipedia.org/wiki/Exome in "FASTQ":https://en.wikipedia.org/wiki/FASTQ_format format and align them to "Chromosome 19":https://en.wikipedia.org/wiki/Chromosome_19_%28human%29 using the "bwa mem":http://bio-bwa.sourceforge.net/ tool, producing a "Sequence Alignment/Map (SAM)":https://samtools.github.io/ file. This tutorial will introduce the following Arvados features:
-<div class="inside-list">
+<div>
* How to create a new pipeline from an existing template.
* How to browse and select input data for the pipeline and submit the pipeline to run on the Arvados cluster.
* How to access your pipeline results.
@@ -14,13 +14,15 @@ A "pipeline" (sometimes called a "workflow" in other systems) is a sequence of s
notextile. <div class="spaced-out">
+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*.
# 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 genoma (fasta)*. 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 genome (fasta)*.
+# 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.
-# Repeat the previous two steps to set the *Input genome (fastq)* parameter to *<i class="fa fa-fw fa-archive"></i> Tutorial sample exome*.
+# 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.
# 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.
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