Ran linkchecker and fixed links.

diff --git a/doc/_layouts/default.html.liquid b/doc/_layouts/default.html.liquid
index 30049748fa4a869415d31af04a8b8928d02c0903..987f525e23941a8b970f7e6d9941c5a6bf8df189 100644 (file)
--- a/doc/_layouts/default.html.liquid
+++ b/doc/_layouts/default.html.liquid
@@ -58,7 +58,7 @@
       margin-top: -61px;
       }
     </style>
-    <link href="{{ site.baseurl }}/css/bootstrap-responsive.min.css" rel="stylesheet">
+    
     <!-- HTML5 shim, for IE6-8 support of HTML5 elements -->
     <!--[if lt IE 9]>
         <script src="../assets/js/html5shiv.js"></script>

diff --git a/doc/user/topics/tutorial-gatk-variantfiltration.html.textile.liquid b/doc/user/topics/tutorial-gatk-variantfiltration.html.textile.liquid
index 4e9a1ebbbefeedfa61099b5159d40c2eedf1f8f7..f83c19934a56afb70a3dada213c6bf2fc939ecf4 100644 (file)
--- a/doc/user/topics/tutorial-gatk-variantfiltration.html.textile.liquid
+++ b/doc/user/topics/tutorial-gatk-variantfiltration.html.textile.liquid
@@ -10,7 +10,7 @@ This tutorial demonstrates how to use the Genome Analysis Toolkit (GATK) with Ar
 
 h2. Installing GATK
 
-Download the GATK binary tarball[1] -- e.g., @GenomeAnalysisTK-2.6-4.tar.bz2@ -- and "copy it to your Arvados VM":tutorial-keep.html.
+Download the GATK binary tarball[1] -- e.g., @GenomeAnalysisTK-2.6-4.tar.bz2@ -- and "copy it to your Arvados VM":{{site.baseurl}}/user/tutorials/tutorial-keep.html.
 
 <notextile>
 <pre><code>~$ <span class="userinput">arv keep put GenomeAnalysisTK-2.6-4.tar.bz2</span>

diff --git a/doc/user/topics/tutorial-job1.html.textile.liquid b/doc/user/topics/tutorial-job1.html.textile.liquid
index 0e90d9eed7157754a88cbb54e44c87009aa08a29..61eaa639a62f7cb34662ae41a86bac9f10d2d4b9 100644 (file)
--- a/doc/user/topics/tutorial-job1.html.textile.liquid
+++ b/doc/user/topics/tutorial-job1.html.textile.liquid
@@ -34,7 +34,7 @@ EOF
 * @<<EOF@ tells the shell to direct the following lines into the standard input for @cat@ up until it sees the line @EOF@
 * @>the_job@ redirects standard output to a file called @the_job@
 * @"script"@ specifies the name of the script to run.  The script is searched for in the "crunch_scripts/" subdirectory of the @git@ checkout specified by @"script_version"@.
-* @"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, or in the form "repository:branch" (in which case it will take 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.  You can access a list of available @git@ repositories on the Arvados workbench under "Compute %(rarr)&rarr;% Code repositories":http://{{site.arvados_workbench_host}}/repositiories .
+* @"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, or in the form "repository:branch" (in which case it will take 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.  You can access a list of available @git@ repositories on the Arvados workbench under "Compute %(rarr)&rarr;% Code repositories":http://{{site.arvados_workbench_host}}/repositories .
 * @"script_parameters"@ are provided to the script.  In this case, the input is the locator for the collection that we inspected in the previous section.
 
 Use @arv job create@ to actually submit the job.  It should print out a JSON object which describes the newly created job:

diff --git a/doc/user/topics/tutorial-parallel.html.textile.liquid b/doc/user/topics/tutorial-parallel.html.textile.liquid
index 21d9841c7eafdaafc59f0036d3034ae703f5cf52..9d08b6988bbe6bb99d49a0f798aa31958cd5b24a 100644 (file)
--- a/doc/user/topics/tutorial-parallel.html.textile.liquid
+++ b/doc/user/topics/tutorial-parallel.html.textile.liquid
@@ -34,7 +34,7 @@ Next, add the file to @git@ staging, commit and push:
 </code></pre>
 </notextile>
 
-You should now be able to run your new script using Crunch, with "script" referring to our new "parallel-hash.py" script.  We will use a different input from our previous examples.  We will use @887cd41e9c613463eab2f0d885c6dd96+83@ which consists of three files, "alice.txt", "bob.txt" and "carol.txt" (the example collection used previously in "fetching data from Arvados using Keep":tutorial-keep.html).
+You should now be able to run your new script using Crunch, with "script" referring to our new "parallel-hash.py" script.  We will use a different input from our previous examples.  We will use @887cd41e9c613463eab2f0d885c6dd96+83@ which consists of three files, "alice.txt", "bob.txt" and "carol.txt" (the example collection used previously in "fetching data from Arvados using Keep":{{site.baseurl}}/user/tutorials/tutorial-keep.html#dir).
 
 <notextile>
 <pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">cat &gt;~/the_job &lt;&lt;EOF

diff --git a/doc/user/tutorials/tutorial-firstscript.html.textile.liquid b/doc/user/tutorials/tutorial-firstscript.html.textile.liquid
index 2e4883398c5b17806961ba231b1736d38d939df4..97a7547b7175103f32a343616093c9d52ee3c07e 100644 (file)
--- a/doc/user/tutorials/tutorial-firstscript.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-firstscript.html.textile.liquid
@@ -22,7 +22,7 @@ First, you should do some basic configuration for git (you only need to do this
 ~$ <span class="userinput">git config --global user.email <b>you</b>@example.com</span></code></pre>
 </notextile>
 
-On the Arvados Workbench, navigate to "Compute %(rarr)&rarr;% Code repositories":http://{{site.arvados_workbench_host}}/repositiories .  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@git.{{ site.arvados_api_host }}:<b>you</b>.git</code></notextile>.
+On the Arvados Workbench, navigate to "Compute %(rarr)&rarr;% Code repositories":http://{{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@git.{{ site.arvados_api_host }}:<b>you</b>.git</code></notextile>.
 
 Next, on the Arvados virtual machine, clone your git repository:
 
@@ -125,7 +125,7 @@ EOF
 * @"components"@ is a set of scripts that make up the pipeline
 * The component is listed with a human-readable name (@"do_hash"@ in this example)
 * @"script"@ specifies the name of the script to run.  The script is searched for in the "crunch_scripts/" subdirectory of the @git@ checkout specified by @"script_version"@.
-* @"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, or in the form "repository:branch" (in which case it will take 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.  You can access a list of available @git@ repositories on the Arvados workbench under "Compute %(rarr)&rarr;% Code repositories":http://{{site.arvados_workbench_host}}/repositiories .
+* @"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, or in the form "repository:branch" (in which case it will take 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.  You can access a list of available @git@ repositories on the Arvados workbench under "Compute %(rarr)&rarr;% Code repositories":http://{{site.arvados_workbench_host}}//repositories .
 * @"script_parameters"@ describes the parameters for the script.  In this example, there is one parameter called @input@ which is @required@ and is a @Collection@.
 
 Now, use @arv pipeline_template create@ tell Arvados about your pipeline template: