Merge branch '16678-login-tokens-lifetime-config'

[arvados.git] / doc / user / topics / tutorial-gatk-variantfiltration.html.textile.liquid

diff --git a/doc/user/topics/tutorial-gatk-variantfiltration.html.textile.liquid b/doc/user/topics/tutorial-gatk-variantfiltration.html.textile.liquid
index ea608b4bc1c15a278f919abe8f8677e943f39b8c..544ccbd35eec476b86478baa3594a9415bbf86d5 100644 (file)
--- a/doc/user/topics/tutorial-gatk-variantfiltration.html.textile.liquid
+++ b/doc/user/topics/tutorial-gatk-variantfiltration.html.textile.liquid
@@ -3,17 +3,22 @@ layout: default
 navsection: userguide
 title: "Using GATK with Arvados"
 ...
+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
+
+SPDX-License-Identifier: CC-BY-SA-3.0
+{% endcomment %}
 
 This tutorial 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.baseurl}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html*
+{% include 'tutorial_expectations' %}
 
 h2. Installing GATK
 
 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>
+<pre><code>~$ <span class="userinput">arv-put GenomeAnalysisTK-2.6-4.tar.bz2</span>
 c905c8d8443a9c44274d98b7c6cfaa32+94
 </code></pre>
 </notextile>
@@ -87,7 +92,7 @@ Next, you need the GATK Resource Bundle[2].  This may already be available in Ar
 
 h2. Submit a GATK job
 
-The Arvados distribution includes an example crunch script ("crunch_scripts/GATK2-VariantFiltration":https://arvados.org/projects/arvados/repository/revisions/master/entry/crunch_scripts/GATK2-VariantFiltration) that runs the GATK VariantFiltration tool with some default settings.
+The Arvados distribution includes an example crunch script ("crunch_scripts/GATK2-VariantFiltration":https://dev.arvados.org/projects/arvados/repository/revisions/master/entry/crunch_scripts/GATK2-VariantFiltration) that runs the GATK VariantFiltration tool with some default settings.
 
 <notextile>
 <pre><code>~$ <span class="userinput">src_version=76588bfc57f33ea1b36b82ca7187f465b73b4ca4</span>
@@ -149,12 +154,7 @@ Now start a job:
  "is_locked_by_uuid":null,
  "log":null,
  "runtime_constraints":{},
- "tasks_summary":{},
- "dependencies":[
-  "5ee633fe2569d2a42dd81b07490d5d13+82",
-  "c905c8d8443a9c44274d98b7c6cfaa32+94",
-  "d237a90bae3870b3b033aea1e99de4a9+10820"
- ]
+ "tasks_summary":{}
 }
 </code></pre>
 </notextile>