Taverna_User_Guide.ppt

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Taverna_User_Guide.ppt

  1. 1. A Users guide to the Taverna workflow Workbench Paul Fisher [email_address]
  2. 2. Prerequisites - 1 <ul><li>Java </li></ul><ul><li>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: </li></ul><ul><li>http://java.sun.com/javase/downloads/index.jsp </li></ul><ul><li>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. </li></ul><ul><li>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. </li></ul><ul><li>The minimal installation you will need is the standard JDK package. </li></ul><ul><li>Download the desired JDK by following the link on the website and choose a location on your computer to save it to. </li></ul><ul><li>Open the saved file and follow the installation instructions to install Java on your computer </li></ul><ul><li>Restart your computer to complete the installation. </li></ul>
  3. 3. <ul><li>A zip package </li></ul><ul><li>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: </li></ul><ul><li>http://www.7-zip.org/download.html </li></ul><ul><li>You will need to choose the appropriate file to download for your operating system, i.e. Windows, Linux, Apple MAC. </li></ul><ul><li>Choose a location to save the file in and save it. </li></ul><ul><li>Locate your saved file and follow the installation instructions to install it on your computer. </li></ul><ul><li>Restart your computer to complete the installation. </li></ul>Prerequisites - 2
  4. 4. <ul><li>Linux users - Graphviz </li></ul><ul><li>Those who are installing Taverna on Linux will also have to install Graphviz onto the system. This is available at the following URL: </li></ul><ul><li>http:// www.graphviz.org / </li></ul><ul><li>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 </li></ul>Prerequisites - 3
  5. 5. Downloading Taverna <ul><li>Open your usual web browser and go to the Taverna homepage at the following URL: </li></ul><ul><li>http://taverna.sourceforge.net/ </li></ul><ul><li>Find, and follow, the ‘Download’ link at the top of the web page to find the latest version of the Taverna workbench to download. </li></ul><ul><li>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. </li></ul><ul><li>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. </li></ul><ul><li>If you have followed these steps, you should get a box which appears in the browser asking you to save the file being downloaded. </li></ul><ul><li>Choose a location to save the file and click OK. </li></ul>
  6. 6. Unzipping the workbench <ul><li>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. </li></ul><ul><li>Choose to “Unzip/Extract the files”, but not into the current directory. </li></ul><ul><li>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 . </li></ul><ul><li>You can change the name of the folder at this stage, e.g. to “Taverna”. </li></ul><ul><li>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. </li></ul>
  7. 7. Running Taverna <ul><li>Locate you Taverna installation and open the Taverna folder. </li></ul><ul><li>Start Taverna by double clicking on the “ runme.bat ” (Windows users )or “ runme.sh ” (Linux and Mac users). </li></ul><ul><li>If you have successfully installed Java, you should see a dialog box or command window open, shortly followed by the Taverna application. </li></ul><ul><li>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. </li></ul><ul><li>The Taverna workbench consists of 3 main panels for constructing workflows: </li></ul><ul><ul><li>The Available services pane (Top Left side) </li></ul></ul><ul><ul><li>The Advanced Model Explorer pane (Bottom Left side) </li></ul></ul><ul><ul><li>The Diagram pane (Right side) </li></ul></ul>
  8. 8. The 3 Panes of Taverna <ul><li>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. </li></ul><ul><li>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. </li></ul><ul><li>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. </li></ul>
  9. 9. 3 Panes of Taverna Diagram pane Advanced Model Explorer Available services
  10. 10. Opening a Workflow Workflow re-use <ul><li>To open a workflow you will need to load a sample workflow, available at the URL specified below: </li></ul><ul><li>http://workflows.mygrid.org.uk/repository/myGrid/PaulFisher/ </li></ul><ul><li>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_pathway.xml </li></ul><ul><li>You can either save this workflow to your local machine or load it directly from the full URL given, including the file name.xml </li></ul><ul><li>Open the “ File ” Menu at the top of the Workbench </li></ul><ul><li>If you are loading from URL choose the option to “ Open workflow location ”, and paste in the URL specified into the dialog box </li></ul><ul><li>If you are loading from your local machine choose the option to “ Open workflow ”, and locate the directory where you saved the file </li></ul><ul><li>Click OK </li></ul><ul><li>This should load up the workflow into the Advanced Model Explorer (AME) and Diagram window </li></ul><ul><li>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 </li></ul>
  11. 11. Open from URL option Paste in the file location – the URL Populated Diagram Populated AME 1 2 3
  12. 12. Running a workflow <ul><li>Now that you have loaded your workflow you can execute it </li></ul><ul><li>To execute your workflow open the “ File ” Menu at the top of the Workbench </li></ul><ul><li>Choose “ Run Workflow ” from the options given – this will open a pop-up box to input your data </li></ul><ul><li>For the chosen workflow, you should have 3 different input: </li></ul><ul><ul><li>chromosome_name </li></ul></ul><ul><ul><li>start_position </li></ul></ul><ul><ul><li>end_position </li></ul></ul><ul><li>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 </li></ul><ul><li>Enter the following data for each input (without quotes): </li></ul><ul><ul><li>chromosome_name – “17” </li></ul></ul><ul><ul><li>start_position – “28500000” </li></ul></ul><ul><ul><li>end_position – “32500000” </li></ul></ul><ul><li>Once you have entered these details, press the “ Run Workflow ” button at the bottom of the pop-up box </li></ul>
  13. 13. Run Workflow option Input pop-up box Click on input Click on “New Input” 1 2 3 4 Run Workflow 5
  14. 14. Viewing Results <ul><li>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 </li></ul><ul><li>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 </li></ul><ul><ul><li>Green = Completed </li></ul></ul><ul><ul><li>Purple = Currently being executed </li></ul></ul><ul><ul><li>Grey = Awaiting execution </li></ul></ul><ul><li>Once completed, the results will appear as separate tabs at the top of the workflow diagram (indicated in the following diagram as workflow outputs) </li></ul><ul><li>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 ” </li></ul><ul><li>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 </li></ul><ul><li>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 </li></ul><ul><li>Then click ok </li></ul>
  15. 15. Results pane Workflow progress Workflow Outputs Result file 1 2 3 Save results to disk 4
  16. 16. Loading a different Workflow <ul><li>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 </li></ul><ul><li>Click OK and you should get your new workflow to appear in the workbench </li></ul><ul><li>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) </li></ul><ul><li>The old workflow can still be modified, run, and executed while this workflow is open </li></ul><ul><li>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” </li></ul><ul><li>This will reload the original workflow which can be executed or changed if required </li></ul><ul><li>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 </li></ul><ul><li>The input pop-up box can then be obtained again by running the workflow </li></ul>

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