[ARVADOS] created: 80d57cdcc9fcae93da2b507942815d9de6dd3351

git at public.curoverse.com git at public.curoverse.com
Fri May 22 16:13:33 EDT 2015 

        at  80d57cdcc9fcae93da2b507942815d9de6dd3351 (commit)


commit 80d57cdcc9fcae93da2b507942815d9de6dd3351
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Fri May 22 16:13:22 2015 -0400

    6141: Remove hard-coded "https://" from "https://{{site.arvados_workbench_host}}" and require that arvados_workbench_host include the url scheme instead.

diff --git a/doc/_config.yml b/doc/_config.yml
index 1e68f08..48a6a01 100644
--- a/doc/_config.yml
+++ b/doc/_config.yml
@@ -8,7 +8,7 @@
 
 baseurl:
 arvados_api_host: localhost
-arvados_workbench_host: localhost
+arvados_workbench_host: http://localhost
 
 exclude: ["Rakefile", "tmp", "vendor"]
 
diff --git a/doc/index.html.liquid b/doc/index.html.liquid
index 4e951d6..c301b52 100644
--- a/doc/index.html.liquid
+++ b/doc/index.html.liquid
@@ -47,7 +47,7 @@ title: Arvados | Documentation
         <!--<p>-->
       <!--<ol>-->
          <!--<li>-->
-           <!--Go to <a href="https://{{ site.arvados_workbench_host }}/" target="_blank">https://{{ site.arvados_workbench_host }}/</a>-->
+           <!--Go to <a href="{{site.arvados_workbench_host}}/" target="_blank">{{site.arvados_workbench_host}}/</a>-->
         <!--</li><li>-->
           <!--Register with any Google account-->
         <!--</li><li>-->
diff --git a/doc/user/getting_started/workbench.html.textile.liquid b/doc/user/getting_started/workbench.html.textile.liquid
index 54ab71b..6e334ba 100644
--- a/doc/user/getting_started/workbench.html.textile.liquid
+++ b/doc/user/getting_started/workbench.html.textile.liquid
@@ -6,7 +6,7 @@ title: Accessing Arvados Workbench
 
 If you are using the default Arvados instance for this guide, you can Access Arvados Workbench using this link:
 
-<a href="https://{{ site.arvados_workbench_host }}/" target="_blank">https://{{ site.arvados_workbench_host }}/</a>
+<a href="{{site.arvados_workbench_host}}/" target="_blank">{{site.arvados_workbench_host}}/</a>
 
 (If you are using a different Arvados instance than the default for this guide, replace *{{ site.arvados_workbench_host }}* with your private instance in all of the examples in this guide.)
 
diff --git a/doc/user/index.html.textile.liquid b/doc/user/index.html.textile.liquid
index 996eb8a..0967cbc 100644
--- a/doc/user/index.html.textile.liquid
+++ b/doc/user/index.html.textile.liquid
@@ -13,7 +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="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 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.
 
diff --git a/doc/user/reference/api-tokens.html.textile.liquid b/doc/user/reference/api-tokens.html.textile.liquid
index 768c7d1..6132f4c 100644
--- a/doc/user/reference/api-tokens.html.textile.liquid
+++ b/doc/user/reference/api-tokens.html.textile.liquid
@@ -6,7 +6,7 @@ title: "Getting an API token"
 
 The Arvados API token is a secret key that enables the @arv@ command line client to access Arvados with the proper permissions.
 
-Access the Arvados Workbench using this link: "https://{{ site.arvados_workbench_host }}/":https://{{ site.arvados_workbench_host }}/  (Replace @{{ site.arvados_api_host }}@ with the hostname of your local Arvados instance if necessary.)
+Access the Arvados Workbench using this link: "{{site.arvados_workbench_host}}/":{{site.arvados_workbench_host}}/  (Replace @{{ site.arvados_api_host }}@ with the hostname of your local Arvados instance if necessary.)
 
 Open a shell on the system where you want to use the Arvados client. This may be your local workstation, or an Arvados virtual machine accessed with SSH (instructions for "Unix":{{site.baseurl}}/user/getting_started/ssh-access-unix.html#login or "Windows":{{site.baseurl}}/user/getting_started/ssh-access-windows.html#login).
 
diff --git a/doc/user/topics/running-pipeline-command-line.html.textile.liquid b/doc/user/topics/running-pipeline-command-line.html.textile.liquid
index 147fbf0..8c8dd14 100644
--- a/doc/user/topics/running-pipeline-command-line.html.textile.liquid
+++ b/doc/user/topics/running-pipeline-command-line.html.textile.liquid
@@ -10,9 +10,9 @@ This tutorial demonstrates how to use the command line to run the same pipeline
 
 When you use the command line, you must use Arvados unique identifiers to refer to objects.  The identifiers in this example correspond to the following Arvados objects:
 
-* <i class="fa fa-fw fa-gear"></i> "Tutorial align using bwa mem (qr1hi-p5p6p-itzkwxblfermlwv)":https://{{ site.arvados_workbench_host }}/pipeline_templates/qr1hi-p5p6p-itzkwxblfermlwv
-* <i class="fa fa-fw fa-archive"></i> "Tutorial chromosome 19 reference (2463fa9efeb75e099685528b3b9071e0+438)":https://{{ site.arvados_workbench_host }}/collections/2463fa9efeb75e099685528b3b9071e0+438
-* <i class="fa fa-fw fa-archive"></i> "Tutorial sample exome (3229739b505d2b878b62aed09895a55a+142)":https://{{ site.arvados_workbench_host }}/collections/3229739b505d2b878b62aed09895a55a+142
+* <i class="fa fa-fw fa-gear"></i> "Tutorial align using bwa mem (qr1hi-p5p6p-itzkwxblfermlwv)":{{site.arvados_workbench_host}}/pipeline_templates/qr1hi-p5p6p-itzkwxblfermlwv
+* <i class="fa fa-fw fa-archive"></i> "Tutorial chromosome 19 reference (2463fa9efeb75e099685528b3b9071e0+438)":{{site.arvados_workbench_host}}/collections/2463fa9efeb75e099685528b3b9071e0+438
+* <i class="fa fa-fw fa-archive"></i> "Tutorial sample exome (3229739b505d2b878b62aed09895a55a+142)":{{site.arvados_workbench_host}}/collections/3229739b505d2b878b62aed09895a55a+142
 
 Use @arv pipeline run@ to run the pipeline, supplying the inputs to the bwa-mem component on the command line:
 
diff --git a/doc/user/topics/tutorial-job1.html.textile.liquid b/doc/user/topics/tutorial-job1.html.textile.liquid
index 0e8b997..92659ce 100644
--- a/doc/user/topics/tutorial-job1.html.textile.liquid
+++ b/doc/user/topics/tutorial-job1.html.textile.liquid
@@ -34,7 +34,7 @@ EOF
 * @cat@ is a standard Unix utility that writes a sequence of input to standard output.
 * @<<EOF@ tells the shell to direct the following lines into the standard input for @cat@ up until it sees the line @EOF at .
 * @>~/the_job@ redirects standard output to a file called @~/the_job at .
-* @"repository"@ is the name of a Git repository to search for the script version.  You can access a list of available git repositories on the Arvados Workbench under "*Code repositories*":https://{{site.arvados_workbench_host}}/repositories.
+* @"repository"@ is the name of a Git repository to search for the script version.  You can access a list of available git repositories on the Arvados Workbench under "*Code repositories*":{{site.arvados_workbench_host}}/repositories.
 * @"script_version"@ specifies the version of the script that you wish to run.  This can be in the form of an explicit Git revision hash, a tag, or a branch.  Arvados logs the script version that was used in the run, enabling you to go back and re-run any past job with the guarantee that the exact same code will be used as was used in the previous run.
 * @"script"@ specifies the name of the script to run.  The script must be given relative to the @crunch_scripts/@ subdirectory of the Git repository.
 * @"script_parameters"@ are provided to the script.  In this case, the input is the PGP data Collection that we "put in Keep earlier":{{site.baseurl}}/user/tutorials/tutorial-keep.html.
@@ -85,11 +85,11 @@ The job is now queued and will start running as soon as it reaches the front of
 
 h2. Monitor job progress
 
-Go to "*Recent jobs*":https://{{site.arvados_workbench_host}}/jobs in Workbench.  Your job should be near the top of the table.  This table refreshes automatically.  When the job has completed successfully, it will show <span class="label label-success">finished</span> in the *Status* column.
+Go to "*Recent jobs*":{{site.arvados_workbench_host}}/jobs in Workbench.  Your job should be near the top of the table.  This table refreshes automatically.  When the job has completed successfully, it will show <span class="label label-success">finished</span> in the *Status* column.
 
 h2. Inspect the job output
 
-On the "Workbench Dashboard":https://{{site.arvados_workbench_host}}, look for the *Output* column of the *Recent jobs* table.  Click on the link under *Output* for your job to go to the files page with the job output.  The files page lists all the files that were output by the job.  Click on the link under the *file* column to view a file, or click on the download button <span class="glyphicon glyphicon-download-alt"></span> to download the output file.
+On the "Workbench Dashboard":{{site.arvados_workbench_host}}, look for the *Output* column of the *Recent jobs* table.  Click on the link under *Output* for your job to go to the files page with the job output.  The files page lists all the files that were output by the job.  Click on the link under the *file* column to view a file, or click on the download button <span class="glyphicon glyphicon-download-alt"></span> to download the output file.
 
 On the command line, you can use @arv job get@ to access a JSON object describing the output:
 
@@ -156,7 +156,7 @@ This MD5 hash matches the MD5 hash which we "computed earlier":{{site.baseurl}}/
 
 h2. The job log
 
-When the job completes, you can access the job log.  On the Workbench, visit "*Recent jobs*":https://{{site.arvados_workbench_host}}/jobs %(rarr)→% your job's UUID under the *uuid* column %(rarr)→% the collection link on the *log* row.
+When the job completes, you can access the job log.  On the Workbench, visit "*Recent jobs*":{{site.arvados_workbench_host}}/jobs %(rarr)→% your job's UUID under the *uuid* column %(rarr)→% the collection link on the *log* row.
 
 On the command line, the Keep identifier listed in the @"log"@ field from @arv job get@ specifies a collection.  You can list the files in the collection:
 
diff --git a/doc/user/tutorials/running-external-program.html.textile.liquid b/doc/user/tutorials/running-external-program.html.textile.liquid
index 6e29613..3ed6ea6 100644
--- a/doc/user/tutorials/running-external-program.html.textile.liquid
+++ b/doc/user/tutorials/running-external-program.html.textile.liquid
@@ -43,11 +43,11 @@ See the "run-command reference":{{site.baseurl}}/user/topics/run-command.html fo
 
 h2. Running your pipeline
 
-Your new pipeline template should appear at the top of the Workbench "pipeline templates":https://{{ site.arvados_workbench_host }}/pipeline_templates page.  You can run your pipeline "using Workbench":tutorial-pipeline-workbench.html or the "command line.":{{site.baseurl}}/user/topics/running-pipeline-command-line.html
+Your new pipeline template should appear at the top of the Workbench "pipeline templates":{{site.arvados_workbench_host}}/pipeline_templates page.  You can run your pipeline "using Workbench":tutorial-pipeline-workbench.html or the "command line.":{{site.baseurl}}/user/topics/running-pipeline-command-line.html
 
-Test data is available in the "Arvados Tutorial":https://{{ site.arvados_workbench_host }}/projects/qr1hi-j7d0g-u7zg1qdaowykd8d project:
+Test data is available in the "Arvados Tutorial":{{site.arvados_workbench_host}}/projects/qr1hi-j7d0g-u7zg1qdaowykd8d project:
 
-* Choose <i class="fa fa-fw fa-archive"></i> "Tutorial chromosome 19 reference (2463fa9efeb75e099685528b3b9071e0+438)":https://{{ site.arvados_workbench_host }}/collections/2463fa9efeb75e099685528b3b9071e0+438 for the "reference_collection" parameter
-* Choose <i class="fa fa-fw fa-archive"></i> "Tutorial sample exome (3229739b505d2b878b62aed09895a55a+142)":https://{{ site.arvados_workbench_host }}/collections/3229739b505d2b878b62aed09895a55a+142 for the "sample" parameter
+* Choose <i class="fa fa-fw fa-archive"></i> "Tutorial chromosome 19 reference (2463fa9efeb75e099685528b3b9071e0+438)":{{site.arvados_workbench_host}}/collections/2463fa9efeb75e099685528b3b9071e0+438 for the "reference_collection" parameter
+* Choose <i class="fa fa-fw fa-archive"></i> "Tutorial sample exome (3229739b505d2b878b62aed09895a55a+142)":{{site.arvados_workbench_host}}/collections/3229739b505d2b878b62aed09895a55a+142 for the "sample" parameter
 
 For more information and examples for writing pipelines, see the "pipeline template reference":{{site.baseurl}}/api/schema/PipelineTemplate.html
diff --git a/doc/user/tutorials/tutorial-firstscript.html.textile.liquid b/doc/user/tutorials/tutorial-firstscript.html.textile.liquid
index 6fe88fe..ba66188 100644
--- a/doc/user/tutorials/tutorial-firstscript.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-firstscript.html.textile.liquid
@@ -101,4 +101,4 @@ Although the job runs locally, the output of the job has been saved to Keep, the
 </code></pre>
 </notextile>
 
-Running locally is convenient for development and debugging, as it permits a fast iterative development cycle.  Your job run is also recorded by Arvados, and will appear in the *Recent jobs and pipelines* panel on the "Workbench Dashboard":https://{{site.arvados_workbench_host}}.  This provides limited provenance, by recording the input parameters, the execution log, and the output.  However, running locally does not allow you to scale out to multiple nodes, and does not store the complete system snapshot required to achieve reproducibility; to do that you need to "submit a job to the Arvados cluster":{{site.baseurl}}/user/tutorials/tutorial-submit-job.html.
+Running locally is convenient for development and debugging, as it permits a fast iterative development cycle.  Your job run is also recorded by Arvados, and will appear in the *Recent jobs and pipelines* panel on the "Workbench Dashboard":{{site.arvados_workbench_host}}.  This provides limited provenance, by recording the input parameters, the execution log, and the output.  However, running locally does not allow you to scale out to multiple nodes, and does not store the complete system snapshot required to achieve reproducibility; to do that you need to "submit a job to the Arvados cluster":{{site.baseurl}}/user/tutorials/tutorial-submit-job.html.
diff --git a/doc/user/tutorials/tutorial-submit-job.html.textile.liquid b/doc/user/tutorials/tutorial-submit-job.html.textile.liquid
index 7cc4b88..8fd5ad9 100644
--- a/doc/user/tutorials/tutorial-submit-job.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-submit-job.html.textile.liquid
@@ -20,7 +20,7 @@ All Crunch scripts are managed through the Git revision control system.  Before
 ~$ <span class="userinput">git config --global user.email $USER at example.com</span></code></pre>
 </notextile>
 
-On the Arvados Workbench, navigate to "Code repositories":https://{{site.arvados_workbench_host}}/repositories.  You should see a repository with your user name listed in the *name* column.  Next to *name* is the column *push_url*.  Copy the *push_url* value associated with your repository.  This should look like <notextile><code>git at git.{{ site.arvados_api_host }}:$USER/$USER.git</code></notextile>.
+On the Arvados Workbench, navigate to "Code repositories":{{site.arvados_workbench_host}}/repositories.  You should see a repository with your user name listed in the *name* column.  Next to *name* is the column *push_url*.  Copy the *push_url* value associated with your repository.  This should look like <notextile><code>git at git.{{ site.arvados_api_host }}:$USER/$USER.git</code></notextile>.
 
 Next, on the Arvados virtual machine, clone your Git repository:
 
@@ -100,13 +100,13 @@ In the editor, enter the following template:
 
 <notextile> {% code 'tutorial_submit_job' as javascript %} </notextile>
 
-* @"repository"@ is the name of a git repository to search for the script version.  You can access a list of available git repositories on the Arvados Workbench under "Code repositories":https://{{site.arvados_workbench_host}}/repositories.
+* @"repository"@ is the name of a git repository to search for the script version.  You can access a list of available git repositories on the Arvados Workbench under "Code repositories":{{site.arvados_workbench_host}}/repositories.
 * @"script_version"@ specifies the version of the script that you wish to run.  This can be in the form of an explicit Git revision hash, a tag, or a branch (in which case it will use the HEAD of the specified branch).  Arvados logs the script version that was used in the run, enabling you to go back and re-run any past job with the guarantee that the exact same code will be used as was used in the previous run.
 * @"script"@ specifies the filename of the script to run.  Crunch expects to find this in the @crunch_scripts/@ subdirectory of the Git repository.
 * @"runtime_constraints"@ describes the runtime environment required to run the job.  These are described in the "job record schema":{{site.baseurl}}/api/schema/Job.html
 
 h2. Running your pipeline
 
-Your new pipeline template should appear at the top of the Workbench "pipeline templates":https://{{ site.arvados_workbench_host }}/pipeline_templates page.  You can run your pipeline "using Workbench":tutorial-pipeline-workbench.html or the "command line.":{{site.baseurl}}/user/topics/running-pipeline-command-line.html
+Your new pipeline template should appear at the top of the Workbench "pipeline templates":{{site.arvados_workbench_host}}/pipeline_templates page.  You can run your pipeline "using Workbench":tutorial-pipeline-workbench.html or the "command line.":{{site.baseurl}}/user/topics/running-pipeline-command-line.html
 
 For more information and examples for writing pipelines, see the "pipeline template reference":{{site.baseurl}}/api/schema/PipelineTemplate.html

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