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:
+{% include 'crunch1only_begin' %}
+On those sites, the details will be slightly different and the example pipeline might not be available.
+{% include 'crunch1only_end' %}
-<div class="inside-list">
-* How to create a project.
-* How to browse available pipeline templates and create a new pipeline from an existing template.
+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">
-# Start from the *Workbench Dashboard*. You can return to the dashboard by clicking on *<i class="fa fa-lg fa-fw fa-home"></i> Home* in the upper left corner of any Workbench page.
-# Click on <span class="btn btn-sm btn-primary" > <i class="fa fa-fw fa-plus"></i> Add new project</span> on the "My projects" panel. This will direct you to the page for the new project.
-# On the new project page, 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.
+h3. Steps
+
+# 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