A Users guide to the Taverna workflow Workbench

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A Users guide to the Taverna workflow Workbench

• Paul Fisher
• fisherp_at_cs.manchester.ac.uk

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Prerequisites - 1

• Java
• In order to run Taverna on your computer you will
  need to have Java installed. If you do not have
  Java already installed, you can download it from
  this URL
• http//java.sun.com/javase/downloads/index.jsp
• You will have a choice of the download you would
  like. Download the JDK with Java EE packaged up
  too. This will give you the opportunity to
  develop web services and use the ones deployed by
  Java developers at a later date. The Java Runtime
  Environment (JRE) being downloaded should be 1.5
  or later for Taverna to work.
• If you have Java installed, but it is an earlier
  version, you will need to update it to 1.5 or
  later otherwise Taverna will NOT work.
• The minimal installation you will need is the
  standard JDK package.
• Download the desired JDK by following the link on
  the website and choose a location on your
  computer to save it to.
• Open the saved file and follow the installation
  instructions to install Java on your computer
• Restart your computer to complete the
  installation.

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Prerequisites - 2

• A zip package
• You will also need a tool to unzip the downloaded
  workbench. There are various tools available on
  the internet, including WinZip, 7-Zip, and a few
  others. Personally I prefer 7-Zip, which is free
  to and easy use, available at the following URL
• http//www.7-zip.org/download.html
• You will need to choose the appropriate file to
  download for your operating system, i.e. Windows,
  Linux, Apple MAC.
• Choose a location to save the file in and save
  it.
• Locate your saved file and follow the
  installation instructions to install it on your
  computer.
• Restart your computer to complete the
  installation.

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Prerequisites - 3

• Linux users - Graphviz
• Those who are installing Taverna on Linux will
  also have to install Graphviz onto the system.
  This is available at the following URL
• http//www.graphviz.org/
• At the time of writing I have no installation
  instructions for this package, so please refer to
  the user documentation provided on the web site

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Downloading Taverna

• Open your usual web browser and go to the Taverna
  homepage at the following URL
• http//taverna.sourceforge.net/
• Find, and follow, the Download link at the top
  of the web page to find the latest version of the
  Taverna workbench to download.
• Once on the Download page, identify the
  relevant Taverna distribution you need. The
  versions for Windows and Linux should be
  downloaded for these operating systems only. A
  separate installation is needed for Apple MAC
  computers.
• Follow the link to download the workbench. The
  web page should re-direct you to the source forge
  page. You will have to allow pop-ups through your
  browser for the file to download properly. If you
  are using Internet Explorer, right click the
  little bar that appears at the top of the browser
  and choose to allow pop-ups for that web site.
  Firefox users go to the Tools option at the top
  of the screen, and open up the options pane.
  Under the content pane uncheck the box that says
  block pop-ups, and then click OK.
• If you have followed these steps, you should get
  a box which appears in the browser asking you to
  save the file being downloaded.
• Choose a location to save the file and click OK.

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Unzipping the workbench

• Locate your Taverna zip file you have downloaded
  and right click on the icon. You should see some
  options to, including one that accesses the zip
  file program you have on your system.
• Choose to Unzip/Extract the files, but not into
  the current directory.
• You will need to choose a directory in which to
  unzip the files. I recommend somewhere in the
  root drive of your computer so you can easily
  access it, e.g. C\myGrid\ .
• You can change the name of the folder at this
  stage, e.g. to Taverna.
• If you are using Taverna on Linux, please be sure
  that you have the relevant access permissions to
  install and run Taverna in the desired directory.

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Running Taverna

• Locate you Taverna installation and open the
  Taverna folder.
• Start Taverna by double clicking on the
  runme.bat (Windows users )or runme.sh (Linux
  and Mac users).
• If you have successfully installed Java, you
  should see a dialog box or command window open,
  shortly followed by the Taverna application.
• Once you have installed Taverna for the first
  time it will need to update all of its
  components. You do not need to do anything for
  this, as this happens as the workbench is
  opening. You should see a graphic in the centre
  of your screen, with a download progress. Each
  component will be shown loading in this progress
  bar in turn. Once this has completed (depending
  on connection speed about 5 minutes), the
  Taverna workbench will open.
• The Taverna workbench consists of 3 main panels
  for constructing workflows
• The Available services pane (Top Left side)
• The Advanced Model Explorer pane (Bottom Left
  side)
• The Diagram pane (Right side)

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The 3 Panes of Taverna

• The Available services pane is used to display
  the web services to the user. This list contains
  default services from when the workbench starts.
  Once you become more experienced with the
  workbench, you will be able to add you own
  services, including adding default services so
  they load automatically when Taverna opens. This
  list contains WSDL web services, local BioJava
  widgets, Soaplab services, and BioMoby objects.
  Each of these can be added to the workflow model
  (workflow being constructed) so that a task can
  be achieved.
• The Advanced Model Explorer pane contains the
  services used in the current workflow, including
  the inputs, outputs, and data links between each
  service. Once populated with services, each
  service can be expanded using the button.
  This provides a list of the inputs and outputs
  that the service takes in and expels. It is these
  inputs and outputs that allow you to connect
  services together.
• The Diagram pane shows a graphical representation
  of the workflow being used/constructed. The
  diagram can be adapted to view different aspects
  of the current workflow, to show all the ports
  for all the services, only those ports that have
  been connected or bound, or to change the layout
  of the workflow from portrait to landscape.

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3 Panes of Taverna
Available services
Diagram pane
Advanced Model Explorer
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Opening a Workflow Workflow re-use

• To open a workflow you will need to load a sample
  workflow, available at the URL specified below
• http//workflows.mygrid.org.uk/repository/myGrid/P
  aulFisher/
• Locate the workflow named qtl_pathway.xml and
  click on the link to see the xml based Scufl text
  - An alternative can be found at
  http//www.cs.man.ac.uk/fisherp/workflows/qtl_pat
  hway.xml
• You can either save this workflow to your local
  machine or load it directly from the full URL
  given, including the file name.xml
• Open the File Menu at the top of the Workbench
• If you are loading from URL choose the option to
  Open workflow location, and paste in the URL
  specified into the dialog box
• If you are loading from your local machine choose
  the option to Open workflow, and locate the
  directory where you saved the file
• Click OK
• This should load up the workflow into the
  Advanced Model Explorer (AME) and Diagram window
• You also notice that some extra services have
  been added to the Available services panel this
  allows you to use additional services if you do
  not have them by default

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1
Open from URL option
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Populated Diagram
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Paste in the file location the URL
Populated AME
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Running a workflow

• Now that you have loaded your workflow you can
  execute it
• To execute your workflow open the File Menu at
  the top of the Workbench
• Choose Run Workflow from the options given
  this will open a pop-up box to input your data
• For the chosen workflow, you should have 3
  different input
• chromosome_name
• start_position
• end_position
• Each of these requires you to enter data to
  enter data into each of the inputs, click on one
  input and then click on the New Data option in
  the pop-up menu system
• Enter the following data for each input (without
  quotes)
• chromosome_name 17
• start_position 28500000
• end_position 32500000
• Once you have entered these details, press the
  Run Workflow button at the bottom of the pop-up
  box

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1
Run Workflow option
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Click on input
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Input pop-up box
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Click on New Input
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Run Workflow
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Viewing Results

• Once you have executed the workflow, the Taverna
  workbench will change views from Design to
  Results. You should see this change behind you
  Input pop-up box
• You can minimise the Input pop-up box to view the
  progress of the workflow being executed the
  different colours indicate whether a service has
  run or not
• Green Completed
• Purple Currently being executed
• Grey Awaiting execution
• Once completed, the results will appear as
  separate tabs at the top of the workflow diagram
  (indicated in the following diagram as workflow
  outputs)
• Each tab contains an output file of results the
  results can be viewed by clicking on the file in
  the left hand pane where it says click to view
• The file can then be searched through using the
  right hand pane, allowing you to verify the
  results if they are wrong simply maximise the
  pop-up window and hit the Run workflow button
  again, making sure that the inputs are correct
• Each file can then be saved to the local machine
  to do this simply click on the button marked
  Save to disk and enter the location to save the
  files
• Then click ok

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Results pane
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Workflow Outputs
Workflow progress
Result file
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Save results to disk
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Loading a different Workflow

• To load a different workflow simply follow the
  same procedure as directed earlier (open from URL
  or open from local directory) changing the
  workflow file to the one that is to be uploaded
• Click OK and you should get your new workflow to
  appear in the workbench
• This workflow can then be executed using the same
  procedure as mentioned earlier (run workflow
  option in the file menu, and enter the new data
  for each input)
• The old workflow can still be modified, run, and
  executed while this workflow is open
• To do this find the Workflows option in the
  menu system at the top of the workbench, then
  click on the workflow loaded previously (hint
  the previous workflow was called Pathways and
  Gene annotations for QTL phenotype
• This will reload the original workflow which can
  be executed or changed if required
• Note to save on space in your browser, I
  recommend you close the input pop-up box once you
  have obtained all the results you need for that
  particular workflow
• The input pop-up box can then be obtained again
  by running the workflow