title: "Running a pipeline using Workbench"
...
+A "pipeline" (sometimes called a "workflow" in other systems) is 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 an 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 will introduce the following Arvados features:
+
+<div class="inside-list">
+* How to create a project.
+* How to browse available pipeline templates and 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":http://{{ site.arvados_workbench_host }}/collections .
-# On the collections page, go to the search box <span class="glyphicon glyphicon-search"></span> and search for "tutorial".
-# This should yield 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. Click on the paperclip <span class="glyphicon glyphicon-paperclip"></span> in the upper right to get a dropdown menu listing your current selections.
-# Go to "Pipeline templates":http://{{ site.arvados_workbench_host }}/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 *parameter* look for "input". Set the value of "input" by clicking on on "none" to get a editing popup. At the top of the selection list in the editing popup will be the collection that you selected in step 4.
-# You can now click on "Run pipeline" in the upper right to start the pipeline.
-# This will reload the page with the pipeline queued to run.
-# The page refreshes automatically every 15 seconds. You should see the pipeline running, and then finish successfully.
-# Once it 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.
-# On the collection page, click on the "Provenance graph" tab to see a graphical representation of the data elements and pipelines that were involved in generating this file.
+# Starting from the Arvados Dashboard, click on <span class="btn btn-sm btn-primary" > <i class="fa fa-fw fa-plus"></i> Add new project</span>. This will direct you to the page for the new project.
+# Click on the pencil icon <i class="fa fa-fw fa-pencil"></i> next to *New project* to pop up a text box and change the project title to *Tutorial output*. Click on <span class="btn btn-xs btn-primary" ><i class="glyphicon glyphicon-ok"></i></span> to save the new name.
+# Click on <span class="btn btn-sm btn-primary"><i class="fa fa-fw fa-gear"></i> Run a pipeline...</span> This will open a modal dialog box titled *Choose a pipeline to run*.
+# Click on *<i class="fa fa-lg fa-fw fa-home"></i> Projects <span class="caret"></span>*. Under *Projects shared with me* select *<i class="fa fa-fw fa-share-alt"></i> Arvados Tutorial*.
+# Select *<i class="fa fa-fw fa-gear"></i> Tutorial align using bwa mem* and click on <span class="btn btn-sm btn-primary" >Next: choose inputs <i class="fa fa-fw fa-arrow-circle-right"></i></span>. This will load a new page where you will supply the inputs for the pipeline.
+# Click on <span class="btn btn-sm btn-primary" >Choose</span> under the first input parameter to the pipeline *reference_collection*. This will open a modal dialog box titled *Choose a dataset*.
+# Once again click on *<i class="fa fa-lg fa-fw fa-home"></i> Projects <span class="caret"></span>* and under *Projects shared with me* select *<i class="fa fa-fw fa-share-alt"></i> Arvados Tutorial*. Select *<i class="fa fa-fw fa-archive"></i> Tutorial chromosome 19 reference* and click on <span class="btn btn-sm btn-primary" >OK</span>.
+# Repeat the previous step to supply the *sample* parameter, this time choosing *<i class="fa fa-fw fa-archive"></i> Tutorial sample exome*.
+# Click on <span class="btn btn-sm btn-primary" >Run <i class="fa fa-fw fa-play"></i></span>.
+# This will refresh the page. The pipeline will be queued and shortly start running. You can track the progress by watching log messages from jobs. This page refreshes automatically. You will see <span class="label label-success">success</span> under the *job* the column when the pipeline completes successfully.
+# Click on *<i class="fa fa-fw fa-archive"></i> Show output files* to see the results of the job. This will load a new page listing the output files from this pipeline. Under the *Files* tab will be the output SAM file from the alignment tool
+# Click on the download icon <span class="btn btn-sm btn-info"><i class="fa fa-download"></i></span> to the right of the SAM file download your results.
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projects / arvados.git / blobdiff