X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/80d57cdcc9fcae93da2b507942815d9de6dd3351..409d130ddcc4b76def5fa8d61d2584725c61152a:/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 8c8dd149b7..c4d3d296af 100644 --- a/doc/user/topics/running-pipeline-command-line.html.textile.liquid +++ b/doc/user/topics/running-pipeline-command-line.html.textile.liquid @@ -1,12 +1,17 @@ --- layout: default navsection: userguide -title: "Running a pipeline on the command line" +title: "Running an Arvados pipeline" ... -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 'crunch1only_begin' %} +If the Jobs API is not available, use the "Common Workflow Language":{{site.baseurl}}/user/cwl/cwl-runner.html instead. +{% include 'crunch1only_end' %} + +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-workflow-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 +37,10 @@ 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