title: "Running a pipeline using Workbench"
...
+{% include 'crunch1only_begin' %}
+On those sites, the details will be slightly different and the example pipeline might not be available.
+{% include 'crunch1only_end' %}
+
+A "pipeline" (sometimes called a "workflow" in other systems) is a sequence of steps that apply various programs or tools to transform input data to output data. Pipelines are the principal means of performing computation with Arvados. This tutorial demonstrates how to run a single-stage pipeline to take a small data set of paired-end reads from a sample "exome":https://en.wikipedia.org/wiki/Exome in "FASTQ":https://en.wikipedia.org/wiki/FASTQ_format format and align them to "Chromosome 19":https://en.wikipedia.org/wiki/Chromosome_19_%28human%29 using the "bwa mem":http://bio-bwa.sourceforge.net/ tool, producing a "Sequence Alignment/Map (SAM)":https://samtools.github.io/ file. This tutorial will introduce the following Arvados features:
+
+<div>
+* How to create a new pipeline from an existing template.
+* How to browse and select input data for the pipeline and submit the pipeline to run on the Arvados cluster.
+* How to access your pipeline results.
+</div>
+
notextile. <div class="spaced-out">
-# Go to "Collections":https://{{ site.arvados_workbench_host }}/collections (*Data* %(rarr)→% *Collections (data files)*).
-# On the Collections page, go to the search box <span class="glyphicon glyphicon-search"></span> and search for "tutorial".
-# The results should include a collection with the contents *var-GS000016015-ASM.tsv.bz2*.
-# Click on the check box to the left of *var-GS000016015-ASM.tsv.bz2*. This puts the collection in your persistent selection list. You can click on the paperclip <span class="glyphicon glyphicon-paperclip"></span> in the upper right to review your current selections.
-# Go to "Pipeline templates":https://{{ site.arvados_workbench_host }}/pipeline_templates (*Compute* %(rarr)→% *Pipeline templates*).
-# Look for a pipeline named *Tutorial pipeline*.
-# Click on the play button <span class="glyphicon glyphicon-play"></span> to the left of *Tutorial pipeline*. This will take you to a new page to configure the pipeline.
-# Under the *parameter* column, look for *input*. Set the value of *input* by clicking on *none* to get a selection popup. The collection that you selected in step 4 will be at the top of that pulldown menu. Select that collection in the pulldown menu.
-# You can now click on the *Run pipeline* button in the upper right to start the pipeline. A new page shows the pipeline status, queued to run.
-# The page refreshes automatically every 15 seconds. You should see the pipeline running, and then finish successfully.
-# Once the pipeline is finished, click on the link under the *output* column. This will take you to the collection page for the output of this pipeline.
-# Click on *md5sum.txt* to see the actual file that is the output of this pipeline.
-# Go back to the collection page for the result. Click on the *Provenance graph* tab to see a graph illustrating the collections and scripts that were used to generate this file.
+h3. Steps
-notextile. </div>
+# Start from the *Workbench Dashboard*. You can access the Dashboard by clicking on *<i class="fa fa-lg fa-fw fa-dashboard"></i> Dashboard* in the upper left corner of any Workbench page.
+# Click on the <span class="btn btn-sm btn-primary"><i class="fa fa-fw fa-gear"></i> Run a pipeline...</span> button. This will open a dialog box titled *Choose a pipeline to run*.
+# In the search box, type in *Tutorial align using bwa mem*.
+# Select *<i class="fa fa-fw fa-gear"></i> Tutorial align using bwa mem* and click the <span class="btn btn-sm btn-primary" >Next: choose inputs <i class="fa fa-fw fa-arrow-circle-right"></i></span> 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 <span class="btn btn-sm btn-primary">Choose</span> 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*.
+# Open the *Home <span class="caret"></span>* menu and select *All Projects*. Search for and select *<i class="fa fa-fw fa-archive"></i> Tutorial chromosome 19 reference* and click the <span class="btn btn-sm btn-primary" >OK</span> button.
+# Repeat the previous two steps to set the *"sample" parameter for run-command script in bwa-mem component* parameter to *<i class="fa fa-fw fa-archive"></i> Tutorial sample exome*.
+# Click on the <span class="btn btn-sm btn-primary" >Run <i class="fa fa-fw fa-play"></i></span> 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 <span class="label label-success">complete</span> 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 <span class="btn btn-sm btn-info"><i class="fa fa-download"></i></span> download button to the right of the SAM file to download your results.
+notextile. </div>
projects / arvados.git / blobdiff