X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/53b19718f974e7c9014644ce80fa36363ae0b693..cac5db66cba0d5dd97c8434853bcbf2ab19fbda5:/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid diff --git a/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid b/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid index f9522fbef0..fac573aca9 100644 --- a/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid +++ b/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid @@ -18,13 +18,13 @@ h3. Steps # Start from the *Workbench Dashboard*. You can access the Dashboard by clicking on * Dashboard* in the upper left corner of any Workbench page. # Click on the Run a pipeline... button. This will open a dialog box titled *Choose a pipeline to run*. -# Click to open the *All projects * menu. Under the *Projects shared with me* header, select * Arvados Tutorial*. +# In the search box, type in *Tutorial align using bwa mem*. # Select * Tutorial align using bwa mem* and click the Next: choose inputs button. This will create a new pipeline in your *Home* project and will open it. You can now supply the inputs for the pipeline. # The first input parameter to the pipeline is *"reference_collection" parameter for run-command script in bwa-mem component*. Click the Choose button beneath that header. This will open a dialog box titled *Choose a dataset for "reference_collection" parameter for run-command script in bwa-mem component*. -# Once again, open the *All projects * menu and select * Arvados Tutorial*. Select * Tutorial chromosome 19 reference* and click the OK button. +# Open the *Home * menu and select *All Projects*. Search for and select * Tutorial chromosome 19 reference* and click the OK button. # Repeat the previous two steps to set the *"sample" parameter for run-command script in bwa-mem component* parameter to * Tutorial sample exome*. # Click on the Run button. The page updates to show you that the pipeline has been submitted to run on the Arvados cluster. -# After the pipeline starts running, you can track the progress by watching log messages from jobs. This page refreshes automatically. You will see a complete label under the *job* column when the pipeline completes successfully. +# After the pipeline starts running, you can track the progress by watching log messages from jobs. This page refreshes automatically. You will see a complete label when the pipeline completes successfully. # Click on the *Output* link to see the results of the job. This will load a new page listing the output files from this pipeline. You'll see the output SAM file from the alignment tool under the *Files* tab. # Click on the download button to the right of the SAM file to download your results.