2525: example param parsing

[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 d01703e96e205a1974efe099ac26c05ec9ca11cb..0248325f61034511acefe6733a9e3d5a8b5f3d8c 100644 (file)
--- a/doc/user/topics/tutorial-gatk-variantfiltration.html.textile.liquid
+++ b/doc/user/topics/tutorial-gatk-variantfiltration.html.textile.liquid
@@ -4,15 +4,13 @@ navsection: userguide
 title: "Using GATK with Arvados"
 ...
 
-h1. 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*
 
 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>
@@ -99,6 +97,7 @@ The Arvados distribution includes an example crunch script ("crunch_scripts/GATK
 ~$ <span class="userinput">cat &gt;the_job &lt;&lt;EOF
 {
  "script":"GATK2-VariantFiltration",
+ "repository":"arvados",
  "script_version":"$src_version",
  "script_parameters":
  {