X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/e86868d96caea7af41140e9d3e26f40b144a0ff6..bd8bdd90055d61263eff5bdb9a953c57319aa83d:/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 f83c19934a..544ccbd35e 100644
--- 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>
@@ -97,6 +102,7 @@ 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":"$src_version",
  "script_parameters":
  {
@@ -148,53 +154,8 @@ Now start a job:
  "is_locked_by_uuid":null,
  "log":null,
  "runtime_constraints":{},
- "tasks_summary":{},
- "dependencies":[
-  "5ee633fe2569d2a42dd81b07490d5d13+82",
-  "c905c8d8443a9c44274d98b7c6cfaa32+94",
-  "d237a90bae3870b3b033aea1e99de4a9+10820"
- ],
- "log_stream_href":"https://qr1hi.arvadosapi.com/arvados/v1/jobs/qr1hi-8i9sb-n9k7qyp7bs5b9d4/log_tail_follow"
+ "tasks_summary":{}
 }
-~$ <span class="userinput">arv job log_tail_follow --uuid qr1hi-8i9sb-n9k7qyp7bs5b9d4</span>
-Tue Dec 17 19:02:16 2013 salloc: Granted job allocation 1251
-Tue Dec 17 19:02:17 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  check slurm allocation
-Tue Dec 17 19:02:17 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  node compute13 - 8 slots
-Tue Dec 17 19:02:17 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  start
-Tue Dec 17 19:02:17 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  Install revision 76588bfc57f33ea1b36b82ca7187f465b73b4ca4
-Tue Dec 17 19:02:18 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  Clean-work-dir exited 0
-Tue Dec 17 19:02:19 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  Install exited 0
-Tue Dec 17 19:02:19 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  script GATK2-VariantFiltration
-Tue Dec 17 19:02:19 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  script_version 76588bfc57f33ea1b36b82ca7187f465b73b4ca4
-Tue Dec 17 19:02:19 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  script_parameters {"input":"5ee633fe2569d2a42dd81b07490d5d13+82","gatk_bundle":"d237a90bae3870b3b033aea1e99de4a9+10820","gatk_binary_tarball":"c905c8d8443a9c44274d98b7c6cfaa32+94"}
-Tue Dec 17 19:02:19 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  runtime_constraints {"max_tasks_per_node":0}
-Tue Dec 17 19:02:19 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  start level 0
-Tue Dec 17 19:02:19 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  status: 0 done, 0 running, 1 todo
-Tue Dec 17 19:02:19 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867 0 job_task qr1hi-ot0gb-d3sjxerucfbvyev
-Tue Dec 17 19:02:19 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867 0 child 4946 started on compute13.1
-Tue Dec 17 19:02:19 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  status: 0 done, 1 running, 0 todo
-Tue Dec 17 19:02:20 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867 0 child 4946 on compute13.1 exit 0 signal 0 success=true
-Tue Dec 17 19:02:20 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867 0 success in 1 seconds
-Tue Dec 17 19:02:20 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867 0 output
-Tue Dec 17 19:02:20 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  wait for last 0 children to finish
-Tue Dec 17 19:02:20 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  status: 1 done, 0 running, 1 todo
-Tue Dec 17 19:02:20 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  start level 1
-Tue Dec 17 19:02:20 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  status: 1 done, 0 running, 1 todo
-Tue Dec 17 19:02:20 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867 1 job_task qr1hi-ot0gb-w8ujbnulxjaamxf
-Tue Dec 17 19:02:20 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867 1 child 4984 started on compute13.1
-Tue Dec 17 19:02:20 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  status: 1 done, 1 running, 0 todo
-Tue Dec 17 19:04:10 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867 1 child 4984 on compute13.1 exit 0 signal 0 success=true
-Tue Dec 17 19:04:10 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867 1 success in 110 seconds
-Tue Dec 17 19:04:10 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867 1 output bedd6ff56b3ae9f90d873b1fcb72f9a3+91
-Tue Dec 17 19:04:10 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  wait for last 0 children to finish
-Tue Dec 17 19:04:10 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  status: 2 done, 0 running, 0 todo
-Tue Dec 17 19:04:10 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  release job allocation
-Tue Dec 17 19:04:10 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  Freeze not implemented
-Tue Dec 17 19:04:10 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  collate
-Tue Dec 17 19:04:10 2013 salloc: Job allocation 1251 has been revoked.
-Tue Dec 17 19:04:10 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  output bedd6ff56b3ae9f90d873b1fcb72f9a3+91
-Tue Dec 17 19:04:11 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  finish
-Tue Dec 17 19:04:12 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867  log manifest is 1e77aaceee2df499e14dc5dde5c3d328+91
 </code></pre>
 </notextile>