[ARVADOS] updated: 94eca7452812a90d68dd29dc62fe2ac5c5157568
git at public.curoverse.com
git at public.curoverse.com
Fri Feb 28 21:35:31 EST 2014
Summary of changes:
doc/_config.yml | 2 +-
doc/_includes/_navbar_top.liquid | 10 +++++-----
doc/install/install-api-server.html.md.liquid | 12 +++++++-----
doc/sdk/python/sdk-python.html.textile.liquid | 2 +-
.../check-environment.html.textile.liquid | 6 +++---
doc/user/reference/api-tokens.html.textile.liquid | 2 +-
doc/user/reference/sdk-cli.html.textile.liquid | 2 +-
.../running-external-program.html.textile.liquid | 2 +-
.../tutorial-firstscript.html.textile.liquid | 2 +-
...rial-gatk-variantfiltration.html.textile.liquid | 2 +-
.../tutorial-job-debug.html.textile.liquid | 2 +-
.../tutorials/tutorial-job1.html.textile.liquid | 2 +-
.../tutorials/tutorial-keep.html.textile.liquid | 2 +-
.../tutorial-new-pipeline.html.textile.liquid | 2 +-
.../tutorial-parallel.html.textile.liquid | 2 +-
.../tutorial-trait-search.html.textile.liquid | 2 +-
16 files changed, 28 insertions(+), 26 deletions(-)
via 94eca7452812a90d68dd29dc62fe2ac5c5157568 (commit)
from 9a124cfd453548bb447df9513f72809a1fba0433 (commit)
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commit 94eca7452812a90d68dd29dc62fe2ac5c5157568
Author: Peter Amstutz <tetron at cosmos>
Date: Fri Feb 28 21:36:00 2014 -0500
Fixed broken links in documentation that were using {{site.basedoc}} instead of {{site.baseurl}}.
Fixed some other links so that documentation can be browsed from file:///
Made some updates to API server setup guide.
diff --git a/doc/_config.yml b/doc/_config.yml
index 3e40c58..9a95734 100644
--- a/doc/_config.yml
+++ b/doc/_config.yml
@@ -1,5 +1,5 @@
exclude: ["Rakefile", "tmp", "vendor"]
-baseurl: /doc
+baseurl: file:///home/tetron/work/arvados/doc/.site
arvados_api_host: qr1hi.arvadosapi.com
navbar:
diff --git a/doc/_includes/_navbar_top.liquid b/doc/_includes/_navbar_top.liquid
index 9303da2..9123893 100644
--- a/doc/_includes/_navbar_top.liquid
+++ b/doc/_includes/_navbar_top.liquid
@@ -11,11 +11,11 @@
</div>
<div class="collapse navbar-collapse" id="bs-navbar-collapse">
<ul class="nav navbar-nav">
- <li {% if page.navsection == 'userguide' %} class="active" {% endif %}><a href="{{ site.baseurl }}/user/">User Guide</a></li>
- <li {% if page.navsection == 'sdk' %} class="active" {% endif %}><a href="{{ site.baseurl }}/sdk/">SDK Reference</a></li>
- <li {% if page.navsection == 'api' %} class="active" {% endif %}><a href="{{ site.baseurl }}/api/">API Reference</a></li>
- <li {% if page.navsection == 'adminguide' %} class="active" {% endif %}><a href="{{ site.baseurl }}/admin/">Admin Guide</a></li>
- <li {% if page.navsection == 'installguide' %} class="active" {% endif %}><a href="{{ site.baseurl }}/install/">Install Guide</a></li>
+ <li {% if page.navsection == 'userguide' %} class="active" {% endif %}><a href="{{ site.baseurl }}/user/index.html">User Guide</a></li>
+ <li {% if page.navsection == 'sdk' %} class="active" {% endif %}><a href="{{ site.baseurl }}/sdk/index.html">SDK Reference</a></li>
+ <li {% if page.navsection == 'api' %} class="active" {% endif %}><a href="{{ site.baseurl }}/api/index.html">API Reference</a></li>
+ <li {% if page.navsection == 'adminguide' %} class="active" {% endif %}><a href="{{ site.baseurl }}/admin/index.html">Admin Guide</a></li>
+ <li {% if page.navsection == 'installguide' %} class="active" {% endif %}><a href="{{ site.baseurl }}/install/index.html">Install Guide</a></li>
<li><a href="https://arvados.org/" style="padding-left: 2em">arvados.org »</a></li>
</ul>
</div>
diff --git a/doc/install/install-api-server.html.md.liquid b/doc/install/install-api-server.html.md.liquid
index f8d66da..a16e50f 100644
--- a/doc/install/install-api-server.html.md.liquid
+++ b/doc/install/install-api-server.html.md.liquid
@@ -20,9 +20,13 @@ Please follow the instructions on the [Download page](https://arvados.org/projec
## Configure the API server
-First configure the database:
+First install the gems:
cd arvados/services/api
+ bundle install
+
+Next, configure the database:
+
cp config/database.yml.sample config/database.yml
Edit database.yml to your liking and make sure the database and db user exist.
@@ -48,11 +52,9 @@ and put it in config/initializers/secret_token.rb:
Server::Application.config.secret_token = 'your-new-secret-here'
-Finally, edit your
-
- environments/production.rb
+Finally, edit the main configuration:
-file.
+ cp config/environments/production.rb.example config/environments/production.rb
First, you want to make sure that
diff --git a/doc/sdk/python/sdk-python.html.textile.liquid b/doc/sdk/python/sdk-python.html.textile.liquid
index 975d600..911f032 100644
--- a/doc/sdk/python/sdk-python.html.textile.liquid
+++ b/doc/sdk/python/sdk-python.html.textile.liquid
@@ -41,7 +41,7 @@ $ <code class="userinput">sudo python setup.py install</code>
h4. Test installation
-If the SDK is installed and your @ARVADOS_API_HOST@ and @ARVADOS_API_TOKEN@ environment variables are set up correctly (see "api-tokens":{{site.basedoc}}/user/reference/api-tokens.html for details), @import arvados@ should produce no errors:
+If the SDK is installed and your @ARVADOS_API_HOST@ and @ARVADOS_API_TOKEN@ environment variables are set up correctly (see "api-tokens":{{site.baseurl}}/user/reference/api-tokens.html for details), @import arvados@ should produce no errors:
<notextile>
<pre>$ <code class="userinput">python</code>
diff --git a/doc/user/getting_started/check-environment.html.textile.liquid b/doc/user/getting_started/check-environment.html.textile.liquid
index 559133d..6cf35f3 100644
--- a/doc/user/getting_started/check-environment.html.textile.liquid
+++ b/doc/user/getting_started/check-environment.html.textile.liquid
@@ -8,7 +8,7 @@ title: "Checking your environment"
h1. Checking your environment
-First you should "log into an Arvados VM instance":{{site.basedoc}}/user/getting_started/ssh-access.html#login if you have not already done so.
+First you should "log into an Arvados VM instance":{{site.baseurl}}/user/getting_started/ssh-access.html#login if you have not already done so.
If @arv user current@ is able to access the API server, it will print out information about your account. Check that you are able to access the Arvados API server using the following command:
@@ -41,6 +41,6 @@ However, if you receive the following message:
bc. ARVADOS_API_HOST and ARVADOS_API_TOKEN need to be defined as environment variables
-Then follow the instructions for "getting an API token,":{{site.basedoc}}/user/reference/api-tokens.html and try @arv user current@ again.
+Then follow the instructions for "getting an API token,":{{site.baseurl}}/user/reference/api-tokens.html and try @arv user current@ again.
-Once you are able to access the API server, you are ready proceed to the first tutorial: "Storing and retrieving data using Arvados Keep.":{{site.basedoc}}/user/tutorials/tutorial-keep.html
+Once you are able to access the API server, you are ready proceed to the first tutorial: "Storing and retrieving data using Arvados Keep.":{{site.baseurl}}/user/tutorials/tutorial-keep.html
diff --git a/doc/user/reference/api-tokens.html.textile.liquid b/doc/user/reference/api-tokens.html.textile.liquid
index 4c49d4a..d47c1cc 100644
--- a/doc/user/reference/api-tokens.html.textile.liquid
+++ b/doc/user/reference/api-tokens.html.textile.liquid
@@ -14,7 +14,7 @@ Access the Arvados workbench using this link: "https://workbench.{{ site.arvados
(Replace @{{ site.arvados_api_host }}@ with the hostname of your local Arvados instance if necessary.)
-First, open a shell on the system on which you intend to use the Arvados client (this may be your local workstation, or an Arvados VM, refer to "Accessing Arvados over ssh":{{site.basedoc}}/user/getting_started/ssh-access.html ) .
+First, open a shell on the system on which you intend to use the Arvados client (this may be your local workstation, or an Arvados VM, refer to "Accessing Arvados over ssh":{{site.baseurl}}/user/getting_started/ssh-access.html ) .
Click on the user icon <span class="glyphicon glyphicon-user"></span> in the upper right corner to access the user settings menu, and click on the menu item _Manage API token_ to go to the "api client authorizations" page.
diff --git a/doc/user/reference/sdk-cli.html.textile.liquid b/doc/user/reference/sdk-cli.html.textile.liquid
index f8d3a43..6d98957 100644
--- a/doc/user/reference/sdk-cli.html.textile.liquid
+++ b/doc/user/reference/sdk-cli.html.textile.liquid
@@ -7,7 +7,7 @@ title: "Command line interface"
h1. Reference: Command Line Interface
-*First, you should be "logged into an Arvados VM instance":{{site.basedoc}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.basedoc}}/user/getting_started/check-environment.html*
+*First, you should be "logged into an Arvados VM instance":{{site.baseurl}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html*
h3. Usage
diff --git a/doc/user/tutorials/running-external-program.html.textile.liquid b/doc/user/tutorials/running-external-program.html.textile.liquid
index e7819a1..7b31e17 100644
--- a/doc/user/tutorials/running-external-program.html.textile.liquid
+++ b/doc/user/tutorials/running-external-program.html.textile.liquid
@@ -10,7 +10,7 @@ h1. Running external programs
This tutorial demonstrates how to use Crunch to run an external program by writting a wrapper using the Python SDK.
-*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.basedoc}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.basedoc}}/user/getting_started/check-environment.html*
+*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.baseurl}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html*
In this tutorial, you will use the external program @md5sum@ to compute hashes instead of the built-in Python library used in earlier tutorials.
diff --git a/doc/user/tutorials/tutorial-firstscript.html.textile.liquid b/doc/user/tutorials/tutorial-firstscript.html.textile.liquid
index 41f8a84..4c49d19 100644
--- a/doc/user/tutorials/tutorial-firstscript.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-firstscript.html.textile.liquid
@@ -10,7 +10,7 @@ h1. Writing a Crunch script
In this tutorial, we will write the "hash" script demonstrated in the first tutorial.
-*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.basedoc}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.basedoc}}/user/getting_started/check-environment.html*
+*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.baseurl}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html*
This tutorial uses *@you@* to denote your username. Replace *@you@* with your user name in all the following examples.
diff --git a/doc/user/tutorials/tutorial-gatk-variantfiltration.html.textile.liquid b/doc/user/tutorials/tutorial-gatk-variantfiltration.html.textile.liquid
index e522b6e..d69b122 100644
--- a/doc/user/tutorials/tutorial-gatk-variantfiltration.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-gatk-variantfiltration.html.textile.liquid
@@ -10,7 +10,7 @@ h1. Using GATK with Arvados
This tutorials demonstrates how to use the Genome Analysis Toolkit (GATK) with Arvados. In this example we will install GATK and then create a VariantFiltration job to assign pass/fail scores to variants in a VCF file.
-*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.basedoc}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.basedoc}}/user/getting_started/check-environment.html*
+*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.baseurl}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html*
h2. Installing GATK
diff --git a/doc/user/tutorials/tutorial-job-debug.html.textile.liquid b/doc/user/tutorials/tutorial-job-debug.html.textile.liquid
index 38ef3be..2805208 100644
--- a/doc/user/tutorials/tutorial-job-debug.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-job-debug.html.textile.liquid
@@ -10,7 +10,7 @@ h1. Debugging a Crunch script
To test changes to a script by running a job, the change must be pushed into @git@, the job queued asynchronously, and the actual execution may be run on any compute server. As a result, debugging a script can be difficult and time consuming. This tutorial demonstrates using @arv-crunch-job@ to run your job in your local VM. This avoids the job queue and allows you to execute the script from your uncomitted git tree.
-*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.basedoc}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.basedoc}}/user/getting_started/check-environment.html*
+*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.baseurl}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html*
This tutorial uses _you_ to denote your username. Replace _you_ with your user name in all the following examples.
diff --git a/doc/user/tutorials/tutorial-job1.html.textile.liquid b/doc/user/tutorials/tutorial-job1.html.textile.liquid
index 88478bb..b66d2e6 100644
--- a/doc/user/tutorials/tutorial-job1.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-job1.html.textile.liquid
@@ -10,7 +10,7 @@ h1. Running a crunch job
This tutorial introduces the concepts and use of the Crunch job system using the @arv@ command line tool and Arvados Workbench.
-*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.basedoc}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.basedoc}}/user/getting_started/check-environment.html*
+*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.baseurl}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html*
In "retrieving data using Keep,":tutorial-keep.html we downloaded a file from Keep and did some computation with it (specifically, computing the md5 hash of the complete file). While a straightforward way to accomplish a computational task, there are several obvious drawbacks to this approach:
* Large files require significant time to download.
diff --git a/doc/user/tutorials/tutorial-keep.html.textile.liquid b/doc/user/tutorials/tutorial-keep.html.textile.liquid
index e020823..8196363 100644
--- a/doc/user/tutorials/tutorial-keep.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-keep.html.textile.liquid
@@ -11,7 +11,7 @@ h1. Storing and Retrieving data using Arvados Keep
This tutorial introduces you to the Arvados file storage system.
-*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.basedoc}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.basedoc}}/user/getting_started/check-environment.html*
+*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.baseurl}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html*
The Arvados distributed file system is called *Keep*. Keep is a content-addressable file system. This means that files are managed using special unique identifiers derived from the _contents_ of the file, rather than human-assigned file names (specifically, the md5 hash). This has a number of advantages:
* Files can be stored and replicated across a cluster of servers without requiring a central name server.
diff --git a/doc/user/tutorials/tutorial-new-pipeline.html.textile.liquid b/doc/user/tutorials/tutorial-new-pipeline.html.textile.liquid
index 0083166..6094807 100644
--- a/doc/user/tutorials/tutorial-new-pipeline.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-new-pipeline.html.textile.liquid
@@ -10,7 +10,7 @@ h1. Constructing a Crunch pipeline
A pipeline in Arvados is a collection of crunch scripts, in which the output from one script may be used as the input to another script.
-*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.basedoc}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.basedoc}}/user/getting_started/check-environment.html*
+*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.baseurl}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html*
h2. Create a new script
diff --git a/doc/user/tutorials/tutorial-parallel.html.textile.liquid b/doc/user/tutorials/tutorial-parallel.html.textile.liquid
index fde36de..36ccbcb 100644
--- a/doc/user/tutorials/tutorial-parallel.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-parallel.html.textile.liquid
@@ -82,4 +82,4 @@ md5sum.txt
h2. The one job per file pattern
-This example demonstrates how to schedule a new task per file. Because this is a common pattern, the Crunch Python API contains a convenience function to "queue a task for each input file":{{site.basedoc}}/sdk/python/crunch-utility-libraries.html#one_task_per_input which reduces the amount of boilerplate code required to handle parallel jobs.
+This example demonstrates how to schedule a new task per file. Because this is a common pattern, the Crunch Python API contains a convenience function to "queue a task for each input file":{{site.baseurl}}/sdk/python/crunch-utility-libraries.html#one_task_per_input which reduces the amount of boilerplate code required to handle parallel jobs.
diff --git a/doc/user/tutorials/tutorial-trait-search.html.textile.liquid b/doc/user/tutorials/tutorial-trait-search.html.textile.liquid
index 13945ff..6402c7e 100644
--- a/doc/user/tutorials/tutorial-trait-search.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-trait-search.html.textile.liquid
@@ -10,7 +10,7 @@ h1. Querying the Metadata Database
This tutorial introduces the Arvados Metadata Database. The Metadata Database stores information about files in Keep. This example will use the Python SDK to find public WGS (Whole Genome Sequencing) data for people who have reported a certain medical condition.
-*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.basedoc}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.basedoc}}/user/getting_started/check-environment.html*
+*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.baseurl}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html*
In the tutorial examples, three angle brackets (>>>) will be used to denote code to enter at the interactive Python prompt.
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