[ARVADOS] created: f198e6126e38a30288763e8720f3dee1b4805677

Wed Nov 30 15:57:22 EST 2016

at  f198e6126e38a30288763e8720f3dee1b4805677 (commit)


commit f198e6126e38a30288763e8720f3dee1b4805677
Author: radhika <radhika at curoverse.com>
Date:   Wed Nov 30 15:46:02 2016 -0500

    10604: Update the "Running a pipeline using Workbench" to talk about "workflows"

diff --git a/doc/_config.yml b/doc/_config.yml
index 96aea34..a884d38 100644
--- a/doc/_config.yml
+++ b/doc/_config.yml
@@ -28,7 +28,7 @@ navbar:
     - Welcome:
       - user/index.html.textile.liquid
       - user/getting_started/community.html.textile.liquid
-    - Run a pipeline using Workbench:
+    - Run a workflow using Workbench:
       - user/getting_started/workbench.html.textile.liquid
       - user/tutorials/tutorial-pipeline-workbench.html.textile.liquid
     - Access an Arvados virtual machine:
@@ -52,7 +52,7 @@ navbar:
     - Working with git repositories:
       - user/tutorials/add-new-repository.html.textile.liquid
       - user/tutorials/git-arvados-guide.html.textile.liquid
-    - Develop an Arvados pipeline:
+    - Develop an Arvados workflow:
       - user/tutorials/intro-crunch.html.textile.liquid
       - user/tutorials/running-external-program.html.textile.liquid
       - user/topics/crunch-tools-overview.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 37a575c..1565bf5 100644
--- a/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid
@@ -1,35 +1,27 @@
 ---
 layout: default
 navsection: userguide
-title: "Running a pipeline using Workbench"
+title: "Running a workflow 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:
+A "workflow" (sometimes called a "pipeline" in other systems) is a sequence of steps that apply various programs or tools to transform input data to output data.  Workflows are the principal means of performing computation with Arvados.  This tutorial demonstrates how to run a single-stage workflow 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.
+* How to create a new process from an existing workflow.
+* How to browse and select input data for the workflow and submit the process to run on the Arvados cluster.
+* How to access your process results.
 </div>
 
-notextile. <div class="spaced-out">
-
 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 process...</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-primary"><i class="fa fa-fw fa-gear"></i> Run a process...</span> button.  This will open a dialog box titled *Choose a pipeline or workflow to run*.
+# In the search box, type in *Tutorial bwa mem cwl*.
+# Select *<i class="fa fa-fw fa-gear"></i> Tutorial bwa mem cwl* 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 process in your *Home* project and will open it. You can now supply the inputs for the process. Please note that all required inputs are pupulated with default values and you can change them if you prefer.
+# For example, let's see how to change *"reference" parameter* for this workflow. Click the <span class="btn btn-sm btn-primary">Choose</span> button beneath the *"reference" parameter* header.  This will open a dialog box titled *Choose a dataset for "reference" parameter for cwl-runner in bwa-mem.cwl 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*. You will then see a list of files. Select *<i class="fa fa-fw fa-file"></i> 19-fasta.bwt* and click the <span class="btn btn-sm btn-primary" >OK</span> button.
+# Repeat the previous two steps to set the *"read_p1" parameter for cwl-runner script in bwa-mem.cwl component* and *"read_p2" parameter for cwl-runner script in bwa-mem.cwl component*       parameters.
+# 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 process has been submitted to run on the Arvados cluster.
+# After the process starts running, you can track the progress by watching log messages from the component(s).  This page refreshes automatically.  You will see a <span class="label label-success">complete</span> label when the process completes successfully.
+# Click on the *Output* link to see the results of the process.  This will load a new page listing the output files from this process.  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>

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hooks/post-receive
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