-$ arv keep ls -s d237a90bae3870b3b033aea1e99de4a9+10820
+~$ arv keep ls -s d237a90bae3870b3b033aea1e99de4a9+10820
50342 1000G_omni2.5.b37.vcf.gz
1 1000G_omni2.5.b37.vcf.gz.md5
464 1000G_omni2.5.b37.vcf.idx.gz
@@ -94,11 +94,11 @@ 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.
-$ src_version=76588bfc57f33ea1b36b82ca7187f465b73b4ca4
-$ vcf_input=5ee633fe2569d2a42dd81b07490d5d13+82
-$ gatk_binary=c905c8d8443a9c44274d98b7c6cfaa32+94
-$ gatk_bundle=d237a90bae3870b3b033aea1e99de4a9+10820
-$ cat >the_job <<EOF
+~$ src_version=76588bfc57f33ea1b36b82ca7187f465b73b4ca4
+~$ vcf_input=5ee633fe2569d2a42dd81b07490d5d13+82
+~$ gatk_binary=c905c8d8443a9c44274d98b7c6cfaa32+94
+~$ gatk_bundle=d237a90bae3870b3b033aea1e99de4a9+10820
+~$ cat >the_job <<EOF
{
"script":"GATK2-VariantFiltration",
"script_version":"$src_version",
@@ -120,7 +120,7 @@ EOF
Now start a job:
-$ arv -h job create --job "$(cat the_job)"
+~$ arv -h job create --job "$(cat the_job)"
{
"href":"https://qr1hi.arvadosapi.com/arvados/v1/jobs/qr1hi-8i9sb-n9k7qyp7bs5b9d4",
"kind":"arvados#job",
@@ -160,7 +160,7 @@ Now start a job:
],
"log_stream_href":"https://qr1hi.arvadosapi.com/arvados/v1/jobs/qr1hi-8i9sb-n9k7qyp7bs5b9d4/log_tail_follow"
}
-$ arv job log_tail_follow --uuid qr1hi-8i9sb-n9k7qyp7bs5b9d4
+~$ arv job log_tail_follow --uuid qr1hi-8i9sb-n9k7qyp7bs5b9d4
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
@@ -204,7 +204,7 @@ Tue Dec 17 19:04:12 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867 log manifest is 1e77a
Once the job completes, the output can be found in hu34D5B9-exome-filtered.vcf:
-$ arv keep ls bedd6ff56b3ae9f90d873b1fcb72f9a3+91
+~$ arv keep ls bedd6ff56b3ae9f90d873b1fcb72f9a3+91
hu34D5B9-exome-filtered.vcf