+<notextile>
+<pre><code>$ <span class="userinput">arv -h job create --job "$(cat the_job)"</span>
+{
+ "href":"https://qr1hi.arvadosapi.com/arvados/v1/jobs/qr1hi-8i9sb-n9k7qyp7bs5b9d4",
+ "kind":"arvados#job",
+ "etag":"9j99n1feoxw3az448f8ises12",
+ "uuid":"qr1hi-8i9sb-n9k7qyp7bs5b9d4",
+ "owner_uuid":"qr1hi-tpzed-9zdpkpni2yddge6",
+ "created_at":"2013-12-17T19:02:15Z",
+ "modified_by_client_uuid":"qr1hi-ozdt8-obw7foaks3qjyej",
+ "modified_by_user_uuid":"qr1hi-tpzed-9zdpkpni2yddge6",
+ "modified_at":"2013-12-17T19:02:15Z",
+ "updated_at":"2013-12-17T19:02:15Z",
+ "submit_id":null,
+ "priority":null,
+ "script":"GATK2-VariantFiltration",
+ "script_parameters":{
+ "input":"5ee633fe2569d2a42dd81b07490d5d13+82",
+ "gatk_binary_tarball":"c905c8d8443a9c44274d98b7c6cfaa32+94",
+ "gatk_bundle":"d237a90bae3870b3b033aea1e99de4a9+10820"
+ },
+ "script_version":"76588bfc57f33ea1b36b82ca7187f465b73b4ca4",
+ "cancelled_at":null,
+ "cancelled_by_client_uuid":null,
+ "cancelled_by_user_uuid":null,
+ "started_at":null,
+ "finished_at":null,
+ "output":null,
+ "success":null,
+ "running":null,
+ "is_locked_by_uuid":null,
+ "log":null,
+ "runtime_constraints":{},
+ "tasks_summary":{},
+ "dependencies":[
+ "5ee633fe2569d2a42dd81b07490d5d13+82",
+ "c905c8d8443a9c44274d98b7c6cfaa32+94",
+ "d237a90bae3870b3b033aea1e99de4a9+10820"
+ ],
+ "log_stream_href":"https://qr1hi.arvadosapi.com/arvados/v1/jobs/qr1hi-8i9sb-n9k7qyp7bs5b9d4/log_tail_follow"
+}
+$ <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+K@qr1hi
+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+K@qr1hi
+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+K@qr1hi
+</code></pre>
+</notextile>
+
+Once the job completes, the output can be found in hu34D5B9-exome-filtered.vcf:
+
+<notextile>
+$ <span class="userinput">arv keep ls bedd6ff56b3ae9f90d873b1fcb72f9a3+91+K@qr1hi</span>
+hu34D5B9-exome-filtered.vcf
+</code></pre>
+</notextile>
+
+h2. Notes
+
+fn1. "Download the GATK tools":http://www.broadinstitute.org/gatk/download
+
+fn2. "Information about the GATK resource bundle":http://gatkforums.broadinstitute.org/discussion/1213/whats-in-the-resource-bundle-and-how-can-i-get-it and "direct download link":ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/2.5/b37/ (if prompted, submit an empty password)