* Fixed links
authorPeter Amstutz <peter.amstutz@clinicalfuture.com>
Mon, 16 Dec 2013 17:16:22 +0000 (12:16 -0500)
committerPeter Amstutz <peter.amstutz@clinicalfuture.com>
Mon, 16 Dec 2013 17:16:22 +0000 (12:16 -0500)
* Added bootstrap and jquery snapshots

19 files changed:
doc/_includes/parallel_hash_script.py
doc/_layouts/default.html
doc/css/bootstrap-responsive.min.css [new file with mode: 0644]
doc/css/bootstrap.css [moved from doc/bootstrap.css with 100% similarity]
doc/js/bootstrap.min.js [new file with mode: 0644]
doc/js/jquery.min.js [new file with mode: 0644]
doc/user/examples/example-pipeline.textile
doc/user/getting_started/check-environment.textile
doc/user/index.textile
doc/user/reference/api-tokens.textile
doc/user/reference/intro-jobs.textile
doc/user/tutorials/intro-keep.textile
doc/user/tutorials/tutorial-firstscript.textile
doc/user/tutorials/tutorial-gatk-variantfiltration.textile
doc/user/tutorials/tutorial-job-debug.textile
doc/user/tutorials/tutorial-job1.textile
doc/user/tutorials/tutorial-new-pipeline.textile
doc/user/tutorials/tutorial-parallel.textile
doc/user/tutorials/tutorial-trait-search.textile

index 46730cfb95ed020b3524e75d7a2992f5df4f15d7..4601b6b1f83c9d5ef1c2984dbb650018986a7e24 100644 (file)
@@ -49,9 +49,7 @@ if this_task['sequence'] == 0:
 
     # Now tell the Arvados API server that this task executed successfully,
     # even though it doesn't have any output.
-    arvados.api().job_tasks().update(uuid=arvados.current_task()['uuid'],
-                                     body={'success':True}
-                                     ).execute()
+    this_task.set_output(None)
 else:
     # The task sequence was not 0, so it must be a parallel worker task
     # created by the first task
index b2a524e4a57e4023850abcc09c205bd7f5bc0779..d190aef4ce0b84e41665554bbc84ebc611090ed8 100644 (file)
@@ -8,7 +8,7 @@
     <meta name="author" content="">
     <link rel="icon" href="{{ site.baseurl }}/images/favicon.ico" type="image/x-icon">
     <link rel="shortcut icon" href="{{ site.baseurl }}/images/favicon.ico" type="image/x-icon">
-    <link href="{{ site.baseurl }}/bootstrap.css" rel="stylesheet">
+    <link href="{{ site.baseurl }}/css/bootstrap.css" rel="stylesheet">
     <style>
       body {
       padding-top: 41px;
@@ -59,7 +59,7 @@
       color: #d14;
       }
     </style>
-    <link href="//netdna.bootstrapcdn.com/twitter-bootstrap/2.3.1/css/bootstrap-responsive.min.css" rel="stylesheet">
+    <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>
 
     </div>
     {% endif %}
-    <script src="//ajax.googleapis.com/ajax/libs/jquery/1.9.1/jquery.min.js"></script>
-    <script src="//netdna.bootstrapcdn.com/twitter-bootstrap/2.3.1/js/bootstrap.min.js"></script>
+    <script src="{{ site.baseurl }}/js/jquery.min.js"></script>
+    <script src="{{ site.baseurl }}/js/bootstrap.min.js"></script>
     <script>
   (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
   (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
diff --git a/doc/css/bootstrap-responsive.min.css b/doc/css/bootstrap-responsive.min.css
new file mode 100644 (file)
index 0000000..291c98f
--- /dev/null
@@ -0,0 +1,20 @@
+/*!
+ * Bootstrap Responsive v2.3.1
+ *
+ * Copyright 2012 Twitter, Inc
+ * Licensed under the Apache License v2.0
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Designed and built with all the love in the world @twitter by @mdo and @fat.
+ */
+.clearfix{*zoom:1;}.clearfix:before,.clearfix:after{display:table;content:"";line-height:0;}
+.clearfix:after{clear:both;}
+.hide-text{font:0/0 a;color:transparent;text-shadow:none;background-color:transparent;border:0;}
+.input-block-level{display:block;width:100%;min-height:30px;-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box;}
+@-ms-viewport{width:device-width;}.hidden{display:none;visibility:hidden;}
+.visible-phone{display:none !important;}
+.visible-tablet{display:none !important;}
+.hidden-desktop{display:none !important;}
+.visible-desktop{display:inherit !important;}
+@media (min-width:768px) and (max-width:979px){.hidden-desktop{display:inherit !important;} .visible-desktop{display:none !important ;} .visible-tablet{display:inherit !important;} .hidden-tablet{display:none !important;}}@media (max-width:767px){.hidden-desktop{display:inherit !important;} .visible-desktop{display:none !important;} .visible-phone{display:inherit !important;} .hidden-phone{display:none !important;}}.visible-print{display:none !important;}
+@media print{.visible-print{display:inherit !important;} .hidden-print{display:none !important;}}@media (max-width:767px){body{padding-left:20px;padding-right:20px;} .navbar-fixed-top,.navbar-fixed-bottom,.navbar-static-top{margin-left:-20px;margin-right:-20px;} .container-fluid{padding:0;} .dl-horizontal dt{float:none;clear:none;width:auto;text-align:left;} .dl-horizontal dd{margin-left:0;} .container{width:auto;} .row-fluid{width:100%;} .row,.thumbnails{margin-left:0;} .thumbnails>li{float:none;margin-left:0;} [class*="span"],.uneditable-input[class*="span"],.row-fluid [class*="span"]{float:none;display:block;width:100%;margin-left:0;-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box;} .span12,.row-fluid .span12{width:100%;-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box;} .row-fluid [class*="offset"]:first-child{margin-left:0;} .input-large,.input-xlarge,.input-xxlarge,input[class*="span"],select[class*="span"],textarea[class*="span"],.uneditable-input{display:block;width:100%;min-height:30px;-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box;} .input-prepend input,.input-append input,.input-prepend input[class*="span"],.input-append input[class*="span"]{display:inline-block;width:auto;} .controls-row [class*="span"]+[class*="span"]{margin-left:0;} .modal{position:fixed;top:20px;left:20px;right:20px;width:auto;margin:0;}.modal.fade{top:-100px;} .modal.fade.in{top:20px;}}@media (max-width:480px){.nav-collapse{-webkit-transform:translate3d(0, 0, 0);} .page-header h1 small{display:block;line-height:20px;} input[type="checkbox"],input[type="radio"]{border:1px solid #ccc;} .form-horizontal .control-label{float:none;width:auto;padding-top:0;text-align:left;} .form-horizontal .controls{margin-left:0;} .form-horizontal .control-list{padding-top:0;} .form-horizontal .form-actions{padding-left:10px;padding-right:10px;} .media .pull-left,.media .pull-right{float:none;display:block;margin-bottom:10px;} .media-object{margin-right:0;margin-left:0;} .modal{top:10px;left:10px;right:10px;} .modal-header .close{padding:10px;margin:-10px;} .carousel-caption{position:static;}}@media (min-width:768px) and (max-width:979px){.row{margin-left:-20px;*zoom:1;}.row:before,.row:after{display:table;content:"";line-height:0;} .row:after{clear:both;} [class*="span"]{float:left;min-height:1px;margin-left:20px;} .container,.navbar-static-top .container,.navbar-fixed-top .container,.navbar-fixed-bottom .container{width:724px;} .span12{width:724px;} .span11{width:662px;} .span10{width:600px;} .span9{width:538px;} .span8{width:476px;} .span7{width:414px;} .span6{width:352px;} .span5{width:290px;} .span4{width:228px;} .span3{width:166px;} .span2{width:104px;} .span1{width:42px;} .offset12{margin-left:764px;} .offset11{margin-left:702px;} .offset10{margin-left:640px;} .offset9{margin-left:578px;} .offset8{margin-left:516px;} .offset7{margin-left:454px;} .offset6{margin-left:392px;} .offset5{margin-left:330px;} .offset4{margin-left:268px;} .offset3{margin-left:206px;} .offset2{margin-left:144px;} .offset1{margin-left:82px;} .row-fluid{width:100%;*zoom:1;}.row-fluid:before,.row-fluid:after{display:table;content:"";line-height:0;} .row-fluid:after{clear:both;} .row-fluid [class*="span"]{display:block;width:100%;min-height:30px;-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box;float:left;margin-left:2.7624309392265194%;*margin-left:2.709239449864817%;} .row-fluid [class*="span"]:first-child{margin-left:0;} .row-fluid .controls-row [class*="span"]+[class*="span"]{margin-left:2.7624309392265194%;} .row-fluid .span12{width:100%;*width:99.94680851063829%;} .row-fluid .span11{width:91.43646408839778%;*width:91.38327259903608%;} .row-fluid .span10{width:82.87292817679558%;*width:82.81973668743387%;} .row-fluid .span9{width:74.30939226519337%;*width:74.25620077583166%;} .row-fluid .span8{width:65.74585635359117%;*width:65.69266486422946%;} .row-fluid .span7{width:57.18232044198895%;*width:57.12912895262725%;} .row-fluid .span6{width:48.61878453038674%;*width:48.56559304102504%;} .row-fluid .span5{width:40.05524861878453%;*width:40.00205712942283%;} .row-fluid .span4{width:31.491712707182323%;*width:31.43852121782062%;} .row-fluid .span3{width:22.92817679558011%;*width:22.87498530621841%;} .row-fluid .span2{width:14.3646408839779%;*width:14.311449394616199%;} .row-fluid .span1{width:5.801104972375691%;*width:5.747913483013988%;} .row-fluid .offset12{margin-left:105.52486187845304%;*margin-left:105.41847889972962%;} .row-fluid .offset12:first-child{margin-left:102.76243093922652%;*margin-left:102.6560479605031%;} .row-fluid .offset11{margin-left:96.96132596685082%;*margin-left:96.8549429881274%;} .row-fluid .offset11:first-child{margin-left:94.1988950276243%;*margin-left:94.09251204890089%;} .row-fluid .offset10{margin-left:88.39779005524862%;*margin-left:88.2914070765252%;} .row-fluid .offset10:first-child{margin-left:85.6353591160221%;*ma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similarity index 100%
rename from doc/bootstrap.css
rename to doc/css/bootstrap.css
diff --git a/doc/js/bootstrap.min.js b/doc/js/bootstrap.min.js
new file mode 100644 (file)
index 0000000..f6736a8
--- /dev/null
@@ -0,0 +1,7 @@
+/**
+* Bootstrap.js by @fat & @mdo
+* plugins: bootstrap-transition.js, bootstrap-modal.js, bootstrap-dropdown.js, bootstrap-scrollspy.js, bootstrap-tab.js, bootstrap-tooltip.js, bootstrap-popover.js, bootstrap-affix.js, bootstrap-alert.js, bootstrap-button.js, bootstrap-collapse.js, bootstrap-carousel.js, bootstrap-typeahead.js
+* Copyright 2012 Twitter, Inc.
+* http://www.apache.org/licenses/LICENSE-2.0.txt
+*/
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\ No newline at end of file
index b494e86549a033b1bf7f736c5ca689ebc09c4e0b..82fb94b7a23768839ca165a890b561d3ece94848 100644 (file)
@@ -14,8 +14,8 @@ clinical/research question to motivate it_ -->
 
 h3. Prerequisites
 
-* Log in to a VM "using SSH":ssh-access.html
-* Put an "API token":api-tokens.html in your @ARVADOS_API_TOKEN@ environment variable
+* Log in to a VM "using SSH":{{site.basedoc}}/user/getting_started/ssh-access.html
+* Put an "API token":{{site.basedoc}}/user/reference/api-tokens.html in your @ARVADOS_API_TOKEN@ environment variable
 * Put the API host name in your @ARVADOS_API_HOST@ environment variable
 
 If everything is set up correctly, the command @arv -h user current@ will display your account information.
index c28863e1c76fa5e5fbb2c87cb1f498dc3d2e95da..192338f61e63d9a07b1899c70e97c8aebbb30f2b 100644 (file)
@@ -11,7 +11,7 @@ Check that you are able to access the Arvados API server using the following com
 
 notextile. <pre><code>$ <span class="userinput">arv user current</span></code></pre>
 
-If you receive the message "ARVADOS_API_HOST and ARVADOS_API_TOKEN need to be defined as environment variables", follow the instructions for "getting an API token,":api-tokens.html then return to this document.
+If you receive the message "ARVADOS_API_HOST and ARVADOS_API_TOKEN need to be defined as environment variables", follow the instructions for "getting an API token,":{{site.basedoc}}/user/reference/api-tokens.html then return to this document.
 
 When @arv user current@ is able to access the API server, it will print out the unique identifier associated with your account.  Here is an example (you will receive a different identifier):
 
@@ -44,4 +44,4 @@ This unique identifier represents your identity in the Arvados system and is sim
 </code></pre>
 </notextile>
 
-You are now ready proceed to the first tutorial: "Fetching data from Arvados using Keep.":intro-keep.html
+You are now ready proceed to the first tutorial: "Fetching data from Arvados using Keep.":{{site.basedoc}}/user/tutorials/intro-keep.html
index 0fe81c23afef304af9a115f91ff53e265b1d269c..7dbe511d6c668821a042e28f57e527c5ad477d34 100644 (file)
@@ -34,9 +34,9 @@ foo
 </code></pre></li>
 <li>Code blocks inline with text emphasize specific <code>programs</code>, <code>files</code>, or <code>options</code> that are being discussed.</li>
 <li>Bold text emphasizes <b>specific items</b> to look when discussing Arvados Workbench pages.</li>
-<li>A sequence of steps separated by right arrows (%(rarr)&rarr;%) indicate a path the user should follow through the Arvados Workbench to access some piece of information under discussion.  The steps indicate a menu, hyperlink, column name, field name, or other label on the page that guide the user where to look or click.
+<li>A sequence of steps separated by right arrows (<span class="rarr">&rarr;</span>) indicate a path the user should follow through the Arvados Workbench to access some piece of information under discussion.  The steps indicate a menu, hyperlink, column name, field name, or other label on the page that guide the user where to look or click.
 </li>
 </ul>
 </notextile>
 
-Now begin by "accessing the Arvados workbench.":workbench.html
+Now begin by "accessing the Arvados workbench.":getting_started/workbench.html
index 1532e9a3dfd11675fe7f9299a0967c42cd267095..49fd9a402ebb59dedb1a9ceb8ce579c47dc508d4 100644 (file)
@@ -18,7 +18,7 @@ Access the Arvados workbench using this link:
 
 Use the menu to navigate to _Access %(rarr)&rarr;% API Tokens._  There should be one or more rows.  The column *api_token* contains the actual token string that you will use.  Copy the value of *api_token* for the first row onto the clipboard.
 
-Next, open a shell on the system on which you intend to use the Arvados client (refer to "Accessing Arvados over ssh":ssh-access.html ) and enter the following (replace the value of @ARVADOS_API_TOKEN@ with the value you copied from the Workbench):
+Next, open a shell on the system on which you intend to use the Arvados client (refer to "Accessing Arvados over ssh":{{site.basedoc}}/user/getting_started/ssh-access.html ) and enter the following (replace the value of @ARVADOS_API_TOKEN@ with the value you copied from the Workbench):
 
 bc. $ export ARVADOS_API_HOST={{ site.arvados_api_host }}
 $ export ARVADOS_API_TOKEN=2jv9kd1o39t0pcfu7aueem7a1zjxhak73w90tzq3gx0es7j1ld
index 7f9f9687d0b557e7644189a84d083737911a72eb..dd51cbc76c87d6893476aeba86e24293fa87f117 100644 (file)
@@ -2,7 +2,7 @@
 layout: default
 navsection: userguide
 title: "Reference: Jobs"
-navorder: 323
+navorder: 923
 ---
 
 h1. Reference: Jobs
index d4b34f29f75714307d912e1d560fe0d87e640624..920ad0d610c9cb591b2cc786e51d81b14a25da9c 100644 (file)
@@ -9,7 +9,7 @@ h1. Fetching data from Arvados using Keep
 
 This tutorial introduces you to the Arvados file storage system.
 
-*This tutorial assumes that you are "logged into an Arvados VM instance":ssh-access.html#login, and have a "working environment.":check-environment.html*
+*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*
 
 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.
index 554185c010cbfcf3cb8da77c6dcb5455cb95a234..4caec36254dd4151d38de69748723772bf3dcd7c 100644 (file)
@@ -9,7 +9,7 @@ h1. Tutorial: 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":ssh-access.html#login, and have a "working environment.":check-environment.html*
+*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 uses _you_ to denote your username.  Replace _you_ with your user name in all the following examples.
 
index 5083d7470b2b787bef39453dcda7fd0f79683061..06ca3fb18b19be39f8e2a4e9efbcb18f4788e8ab 100644 (file)
@@ -9,18 +9,12 @@ h1. Tutorial: GATK VariantFiltration
 
 Here you will use the GATK VariantFiltration program 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 should be motivated better using a specific biomedical research or diagnostic question that involves this analysis_ -->
 
 <!-- From conversation with Ward:  We should link to a discussion of the personal genome project and explain that it a freely available dataset that any researcher can use, which makes it appropriate to be used in these examples._ -->
 
-h3. Prerequisites
-
-* Log in to a VM "using SSH":ssh-access.html
-* Put an "API token":api-tokens.html in your @ARVADOS_API_TOKEN@ environment variable
-* Put the API host name in your @ARVADOS_API_HOST@ environment variable
-
-If everything is set up correctly, the command @arv -h user current@ will display your account information.
-
 h3. Get the GATK binary distribution.
 
 <!-- _Perhaps separate out this and the next sections and link to it so the user only
index 5dc5ae0a4e2b302fe90956bc1bbc4d8a0e8a76d7..a35bbec2113fe0964af43c0c9ab57f1b48862c72 100644 (file)
@@ -9,7 +9,7 @@ h1. Tutorial: Debug 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":ssh-access.html#login, and have a "working environment.":check-environment.html*
+*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 uses _you_ to denote your username.  Replace _you_ with your user name in all the following examples.
 
index 7b51288c935f4a316d299a5de9cecfdf604f7bc5..81cdcde79638b3ab89b2bad4cc35032b21daccc5 100644 (file)
@@ -9,7 +9,7 @@ h1. Tutorial: 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":ssh-access.html#login, and have a "working environment.":check-environment.html*
+*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*
 
 In the previous section, we downloaded a file from Keep and computed the md5 hash of the complete file.  While straightforward, there are several obvious drawbacks to this approach:
 * Large files require significant time to download.
index 6dbafbc627d9074d2fe24d4c9d95f3f475090ed8..80783746836cf29fc74262fa6b516ae95dc948de 100644 (file)
@@ -9,7 +9,7 @@ h1. Tutorial: Construct a pipeline
 
 A pipeline in Arvados is a sequence of crunch scripts, in which the output from the previous script is fed in as the input to the next script.
 
-*This tutorial assumes that you are "logged into an Arvados VM instance":ssh-access.html#login, and have a "working environment.":check-environment.html*
+*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*
 
 h2. Create a new script
 
index 88785a8dc3ab16293618023514cb47c3ab0ed943..c8601af6173adda0fb1b046438a610030bac2293 100644 (file)
@@ -77,4 +77,4 @@ $ <span class="userinput">arv keep get e2ccd204bca37c77c0ba59fc470cd0f7+162+K@qr
 
 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":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.basedoc}}/user/reference/crunch-utility-libraries.html#one_task_per_input which reduces the amount of boilerplate code required to handle parallel jobs.
index aa36e8a40c42bee0265f3fb320481ea3febf7ca9..be0cdf2e03bcde301752c9797d37545386bb6fd4 100644 (file)
@@ -19,13 +19,7 @@ variant in the people with the reported traits_ -->
 <!-- _Rather than having the user do this through the Python command line,
 it might be easier to write a file that is going to do each step_ -->
 
-
-h3. Prerequisites
-
-* Log in to a VM "using SSH":ssh-access.html
-* Put an "API token":api-tokens.html in your @ARVADOS_API_TOKEN@ environment variable
-* Put the API host name in your @ARVADOS_API_HOST@ environment variable
-* Run the @python@ interactive shell.
+*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*
 
 If everything is set up correctly, you will be able to import the arvados SDK: