X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/1f760632ae0fbb9f11af5cfb831b7c3ed49a7009..f4ca9ad94a6bb006d1f3c7ba207837f1736d1247:/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 ea608b4bc1..c1c9123a59 100644
--- a/doc/user/topics/tutorial-gatk-variantfiltration.html.textile.liquid
+++ b/doc/user/topics/tutorial-gatk-variantfiltration.html.textile.liquid
@@ -6,7 +6,7 @@ title: "Using GATK with Arvados"
 
 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
 
@@ -87,7 +87,7 @@ 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 +149,7 @@ 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>