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>
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>
"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>
projects / arvados.git / blobdiff