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">
-# If you have not yet created any projects, first create a new project to save your work. Please see "Accessing Arvados Workbench":{{site.baseurl}}/user/getting_started/workbench.html page for details. If you already have created a project for your work, go to the project by clicking on the project in *My projects* panel.
-# Click on the <span class="btn btn-primary glyphicon-plus"> Add data...</span> button.
-# In the *Add data to project* popup window, enter *tutorial* in the search box.
-# The results should include a *tutorial* collection.
-# Click on this collection and verify that it is the collection *var-GS000016015-ASM.tsv.bz2*.
-# Click on the <span class="btn btn-primary"> Add </span> button in the popup. This adds the *var-GS000016015-ASM.tsv.bz2* collection to your project.
-# Click on the <span class="btn btn-primary glyphicon-gear"> Run a pipeline... </span> button
-# In the *Choose a pipeline to run* popup window, enter *tutorial* in the search box.
-# The result should include *Tutorial pipeline* template.
-# Click on this template and the click on <span class="btn btn-primary"> Next: choose inputs </span> button. This will take you to a new page to configure the pipeline instance.
-# In the *Inputs* tab, click on <span class="btn btn-primary"> Choose </span> button
-# In the *Choose a dataset* popup, click on the *tutorial* collection and click on <span class="btn btn-primary"> OK </span> button.
-# You can now run this pipeline by clicking on the <span class="btn btn-primary"> Run </span> button.
-# 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 *Show output files* button. 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