X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/dce0ccabe3d9fab6943e89dc84050793cca5b553..7ca020894d276edf9098132f4757cdd46b6b1441:/doc/user/topics/running-pipeline-command-line.html.textile.liquid diff --git a/doc/user/topics/running-pipeline-command-line.html.textile.liquid b/doc/user/topics/running-pipeline-command-line.html.textile.liquid index 147fbf0d3a..8c27fbf18d 100644 --- a/doc/user/topics/running-pipeline-command-line.html.textile.liquid +++ b/doc/user/topics/running-pipeline-command-line.html.textile.liquid @@ -7,6 +7,7 @@ title: "Running a pipeline on the command line" This tutorial demonstrates how to use the command line to run the same pipeline as described in "running a pipeline using Workbench.":{{site.baseurl}}/user/tutorials/tutorial-pipeline-workbench.html {% include 'tutorial_expectations' %} +{% include 'tutorial_cluster_name' %} When you use the command line, you must use Arvados unique identifiers to refer to objects. The identifiers in this example correspond to the following Arvados objects: @@ -32,9 +33,10 @@ bwa-mem qr1hi-8i9sb-67n1qvsronmd2z6 49bae1066f4ebce72e2587a3efa61c7d+88 This instantiates your pipeline and displays periodic status reports in your terminal window. The new pipeline instance will also show up on the Workbench Dashboard. + @arv pipeline run@ submits a job for each pipeline component as soon as the component's inputs are known (i.e., any dependencies are satsified). It terminates when there is no work left to do: this means either all components are satisfied and all jobs have completed successfully, _or_ one or more jobs have failed and it is therefore unproductive to submit any further jobs. -The Keep locators of the output of of the @bwa-mem@ components are available from the last status report shown above: +The Keep locators of the output of the @bwa-mem@ components are available from the last status report shown above: 
~$ arv keep ls -s 49bae1066f4ebce72e2587a3efa61c7d+88