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Posted to commits@taverna.apache.org by bu...@apache.org on 2015/02/09 16:07:28 UTC
svn commit: r939567 - in /websites/staging/taverna/trunk: cgi-bin/ content/
content/documentation/quick-start-guide/
content/documentation/quick-start-guide/index.html
Author: buildbot
Date: Mon Feb 9 15:07:27 2015
New Revision: 939567
Log:
Staging update by buildbot for taverna
Added:
websites/staging/taverna/trunk/content/documentation/quick-start-guide/
websites/staging/taverna/trunk/content/documentation/quick-start-guide/index.html
Modified:
websites/staging/taverna/trunk/cgi-bin/ (props changed)
websites/staging/taverna/trunk/content/ (props changed)
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+<!DOCTYPE html>
+<html lang="en">
+ <head>
+ <meta charset="utf-8">
+ <meta http-equiv="X-UA-Compatible" content="IE=edge">
+ <meta name="viewport" content="width=device-width, initial-scale=1">
+ <title>Apache Taverna - Quick start guide</title>
+
+ <meta http-equiv="Content-Type" content="text/html;charset=UTF-8">
+ <meta property="og:image" content="/img/taverna-logo-145x134.png" />
+
+ <link rel="shortcut icon" href="/favicon.ico">
+ <link rel="icon" type="image/png" sizes="145x134" href="/img/taverna-logo-145x134.png">
+ <link rel="apple-touch-icon" sizes="145x134" href="/img/taverna-logo-145x134.png">
+
+ <link rel="stylesheet" href="/lib/bootstrap/css/bootstrap.min.css">
+ <link rel="stylesheet" href="/lib/bootstrap/css/bootstrap-theme.min.css">
+ <link rel="stylesheet" href="/css/sticky-footer-navbar.css">
+ <link rel="stylesheet" href="/css/taverna.css">
+
+
+
+
+ <!-- Licensed to the Apache Software Foundation (ASF) under one or more contributor license agreements. See the NOTICE file distributed with this work for additional information regarding copyright ownership. The ASF licenses this file to you under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at . http://www.apache.org/licenses/LICENSE-2.0 . Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. -->
+
+ <!-- JSON-LD markup for Google Structured Data -->
+
+ <!-- generic JSON-LD for this page -->
+ <script type="application/ld+json">
+ {
+ "@context" : "http://schema.org",
+ "@type" : ["CreativeWork"],
+ "@id": "",
+ "name" : "Quick start guide",
+ "publisher" : {
+ "@type" : "Organization",
+ "url" : "http://www.apache.org/",
+ "name" : "The Apache Software Foundation (ASF)"
+ },
+ "license": {
+ "@type": "CreativeWork",
+ "@id": "http://www.apache.org/licenses/LICENSE-2.0",
+ "url": "http://www.apache.org/licenses/LICENSE-2.0",
+ "name": "Apache License, Version 2.0"
+ }
+ }
+</script>
+
+ </head>
+
+ <body>
+
+ <!-- Static navbar -->
+ <nav class="navbar navbar-default" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false" aria-controls="navbar">
+ <span class="sr-only">Toggle navigation</span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="/"><img src="/img/taverna-logo-145x134.png" alt="">Apache Taverna</a>
+
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li class="dropdown">
+ <a href="/introduction/" data-toggle="dropdown" role="button" aria-expanded="false">Introduction<span class="caret"></span></a>
+ <ul class="dropdown-menu" role="menu">
+ <li><a href="/introduction/taverna-features">Taverna features</a></li>
+ <li><a href="/introduction/why-use-workflows">Why use workflows?</a></li>
+ <li><a href="/introduction/what-is-in-silico-experimentation">What is âin silicoâ experimentation?</a></li>
+ <li><a href="/introduction/what-is-a-workflow-management-system">What is a Workflow Management System?</a></li>
+ <li><a href="/introduction/how-can-taverna-help-me">How can Taverna help me?</a></li>
+ <li><a href="/introduction/services-in-taverna">Services in Taverna</a></li>
+ <li><a href="/introduction/related-projects">Related projects</a></li>
+ <li><a href="/introduction/chemistry-web-services">Chemistry-web-services</a></li>
+ <li><a href="/introduction/taverna-in-use">Taverna in use</a></li>
+ <li><a href="/introduction/works-with">Works with...</a></li>
+ <li><a href="/introduction/roadmap.html">Raod Map</a></li>
+ </ul>
+ </li>
+ <li class="dropdown">
+ <a href="/documentation" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Documentation<span class="caret"></span></a>
+ <ul class="dropdown-menu" role="menu">
+ <li><a href="/documentation/page1">Page 1</a></li>
+ <li><a href="/documentation/page2">Page 2</a></li>
+ </ul>
+ </li>
+ <li class="dropdown">
+ <a href="/download" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Download<span class="caret"></span></a>
+ <ul class="dropdown-menu" role="menu">
+ <li><a href="/download">Apache Taverna 3.x</a></li>
+ <li><a href="/download/pre-apache">Taverna 2.x (Pre-Apache)</a></li>
+ </ul>
+ </li>
+ <li><a href="/code">Code</a></li>
+ <li class="dropdown">
+ <a href="/community" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Community<span class="caret"></span></a>
+ <ul class="dropdown-menu" role="menu">
+ <li><a href="/community#mailinglists">Mailing Lists</a></li>
+ <li><a href="/community#contribute">Contribute</a></li>
+ <li><a href="/community#reportbugs">Report a Bug</a></li>
+ </ul>
+ </li>
+ </ul>
+
+ <form >
+
+
+ <!--<input type="submit" id="submit" value="Search">-->
+ </form>
+
+ <form class="navbar-form navbar-right" role="search"
+ name="search" id="search" action="http://www.google.com/search" method="get">
+ <input value="taverna.incubator.apache.org" name="sitesearch" type="hidden"/>
+ <div class="form-group input-group">
+ <input type="text" name="q" id="query" placeholder="Search" class="form-control">
+ <span class="input-group-btn">
+ <button type="submit" class="btn btn-default">Search</button>
+ </span>
+ </div>
+ </form>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li class="dropdown">
+ <a href="http://www.apache.org/" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">ASF<span class="caret"></span></a>
+ <ul class="dropdown-menu" role="menu">
+ <li><a href="http://www.apache.org/">Apache Software Foundation</a></li>
+ <li><a href="http://www.apache.org/foundation/how-it-works.html">How it works</a></li>
+ <li><a href="http://www.apache.org/foundation/thanks.html">Thanks</a></li>
+ <li><a href="http://www.apache.org/foundation/sponsorship.html">Become a Sponsor</a></li>
+ <li><a href="http://incubator.apache.org/projects/taverna.html">Taverna Incubation Status</a></li>
+ </ul>
+ </li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container-->
+ </nav>
+
+
+ <div id="page" class="container">
+ <h1>Quick start guide</h1>
+ <div class="alert alert-info" role="alert"><p><span class="glyphicon glyphicon-info-sign" aria-hidden="true"></span>
+
+Taverna is transitioning to the Apache Incubator.
+This webpage reflects material not yet released under Apache Incubator.
+Instead it shows <a class="alert-link" href="http://www.taverna.org.uk/">taverna2</a> material that is expected to become part of the Apache Incubator project in the future.
+</div>
+
+
+ <div id="content"><p>Taverna is a powerful scientific
+ <a href="/introduction/what-is-a-workflow-management-system">workflow management application</a>
+ that allows designing and executing workflows.</p>
+<p><a href="/introduction/why-use-workflows">Scientific workflows</a> help tackle the problem of excessive
+ complexity of <a href="/introduction/what-is-in-silico-experimentation"><em>in silico</em> experimentation</a>
+ by helping scientists model what an experiment is set to achieve,
+ while abstracting out how it will be executed.</p>
+<p>This quick start guide will help you open, create and run a workflow.
+Before you start, you should download the <a href="/download/">Taverna Workbench</a>.</p>
+<p>You should also refer to the
+ <a href="http://www.mygrid.org.uk/dev/wiki/display/taverna/User+Manual">User Manual</a>,
+ which contains a more comprehensive documentation on how to use Taverna.</p>
+<h2 id="opening-an-existing-workflow">Opening an existing workflow</h2>
+<p>It is simple to open an existing workflow inside the Taverna Workbench.<br />
+If you already have a Taverna workflow, go to <em>File ->Open Workflow</em>
+ and navigate to your workflow file (it should be in .t2flow format).</p>
+<p>When you click <em>OK</em>, if the workflow loads correctly, the
+ <a href="/documentation/glossary#workflow_diagram"><em>Workflow Diagram</em></a> and
+ <a href="/documentation/glossary/#workflow_explorer"><em>Workflow Explorer</em></a>
+ panels are populated with the workflow defined in the file.
+There may be a short delay while Taverna contacts the network to get more information about
+ the resources (services) the workflow uses - if the delay is a very long one followed by
+ an error you probably need to check the configuration of your <em>HTTP Proxy Preferences</em>.</p>
+<p>If you do not have an existing workflow, you can download and open one from
+ <a href="http://www.myexperiment.org/"><em>myExperiment</em></a>.
+For bioinformatics examples, go to myExperiment and search for the Pack entitled
+ "<a href="http://www.myexperiment.org/packs/363.html"><em>Bioinformatics Workflow Examples</em></a>".
+From this pack, download the workflow entitled
+ "[<em>Blast_Align_and_Tree</em>]http://www.myexperiment.org/workflows/3369.html_"
+ by selecting it and selecting the Download option "<em>Download Workflow File/Package (T2FLOW</em>)".
+Alternatively, you can copy the link location from the <em>Run</em> section in the workflow entry page.
+If you go to <em>File -> Open Workflow Location... </em>in the workbench, you can paste this
+ <a href="http://www.myexperiment.org/workflows/3369/download?version=1">link</a> directly into the
+ dialogue box.</p>
+<p>To run the workflow, click the green 'play' button at the top of the workbench, or go to
+ <em>File -> Run workflow</em>.
+In the pop-up workflow input box, add the first input (your email address),
+by selecting "<em>set value</em>" and typing it in the box.
+Change to the other input tab (sequence) at the top of the window and add a protein sequence
+ in <em>FASTA</em> format in the same way.
+An example is given and will be automatically added when you click on "set value",
+ but you can add your own instead if you wish.
+To launch the workflow, click "<em>Run workflow</em>" at the bottom of the input window.</p>
+<p>For more general workflow examples, you can find and download workflows from the
+ Taverna starter packs
+ (see <a href="http://www.myexperiment.org/packs/612.html">Taverna 2.5 starter pack</a>
+ for an example set).</p>
+<p>You can additionally access the content of myExperiment directly from the Taverna Workbench by
+ selecting the <em>myExperiment Perspective</em> at the top of the workbench.
+The <em>Starter Pack</em> tab in the myExperiment Perspective contains the current Taverna starter
+ pack of workflows.</p>
+<h2 id="creating-a-workflow">Creating a workflow</h2>
+<p>We will now create and run a very simple Taverna 2.x workflow to list some cities in a country.
+When you start the Workbench up, the default perspective you are presented with is the Design
+ Perspective which is used for creating and editing workflows.
+To start creating a new workflow, choose <em>New workflow</em> from the <em>File</em> menu.</p>
+<h2 id="adding-a-service-into-taverna">Adding a service into Taverna</h2>
+<p>Taverna 2.x does not, by default, âknowâ about a suitable service to perform the desired
+ functionality.
+To add a new <a href="/documentation/glossary/#web_service">Web service</a> click <em>Import new services</em>
+ in the [<em>Service Panel</em>]/documentation/glossary/#service_panel) and then <em>WSDL serviceâ¦</em>.
+Enter the URL of the WSDL, in this case
+"http://www.webservicex.com/globalweather.asmx?WSDL" and click <em>OK</em>.</p>
+<p>After a while, the service will become available in the <em>Service Panel</em>.
+If you filter the services by âglobalweatherâ then you can see the two new services under
+ "WSDL @ http://www.webservicex.com/globalweather.asmx?WSDL".</p>
+<h2 id="adding-a-service-into-the-workflow">Adding a service into the workflow</h2>
+<p>To add a service we have just imported in Taverna into the workflow,
+ click on GetCitiesByCountry in the Service Panel and drag it into the <em>Workflow Diagram</em> or
+ to the tree in the <em>Workflow Explorer</em>.</p>
+<h2 id="creating-the-workflow-inputs">Creating the workflow inputs</h2>
+<p>The workflow needs to have an input, in this case the name of the country to query.
+You can create a new workflow input by right clicking in a blank area of the <em>Workflow Diagram</em>
+ and select <em>Insert</em> -> <em>Workflow input port</em>.
+This will then ask you for a name for the input port, you can change this later but for now use
+ "country".
+Click <em>OK</em> and you should see your new input appear in the <em>Workflow Diagram</em> and
+ <em>Workflow Explorer</em>.</p>
+<p>Similarly, the workflow will need an output.
+Follow an equivalent process but this time clicking on <em>Insert</em> -> <em>Workflow output port</em>
+ and using the name "cities" to create an output.
+Again, you should see the output appear in the two panels of the Workbench.</p>
+<h2 id="splitting-the-wsdl-inputs-and-outputs">Splitting the WSDL inputs and outputs</h2>
+<p>For many services, you can connect their inputs and outputs directly.
+However, for <a href="/documentation/glossary#wsdl">WSDL services</a> you may need to âsplitâ the XML used
+ to hold the input and output values.
+To do this, right-click on the service GetCitiesByCountry in the <em>Workflow Diagram</em> or
+ <em>Workflow Explorer</em> and select <em>Show details</em>.</p>
+<p>A description of the service will appear in the <em>Details</em> view of the <em>Workflow Explorer</em>.
+Scroll down and click both <em>Add input XML splitter</em> and <em>Add output XML splitter</em>,
+ choosing âparametersâ in both cases.</p>
+<h2 id="connecting-everything-together">Connecting everything together</h2>
+<p>To link the input port, click on âcountryâ and drag to the âGetCitiesByCountry_inputâ.
+A connection arrow will appear in the <em>Workflow Diagram</em>.
+If there had been several ports that you could have connected to,
+ then the multiple options would have been offered to you.
+Alternatively, you may right-click the âGetCitiesByCountry_inputâ input port of the service and
+ select <em>Connect with output from...</em> -><em>Workflow input ports</em> and select the
+ "country" workflow input port.</p>
+<p>To connect from the âGetCitiesByCountry_outputâ, right-click on it and select
+ <em>Connect as input to...</em> -><em>Workflow output ports</em> and select the âcitiesâ output port.
+Alternatively, you may start to draw a link (a green arrow will appear) from the
+âGetCitiesByCountry_outputâ output port of the service towards the workflow output port
+ âcitiesâ.</p>
+<h2 id="running-the-workflow">Running the workflow</h2>
+<p>You can now run the workflow you have just created.</p>
+<p>Select <em>Run workflow</em> from the <em>File</em> menu. In the <em>Workflow Inputs Dialog</em>,
+ as there is only one input port, you can click <em>New value </em>button.<br />
+Replace the string âSome input data goes hereâ by your chosen country name.
+After you have entered it, you can click <em>Run workflow</em>.</p>
+<p>Taverna will automatically switch to the <em>Results Perspective</em>.
+The workflow run will be displayed in the <em>Monitor View </em>tabs
+ (either as a graph showing progress or as a progress table).
+This panel shows you the progress of the workflow - running services are shown green and
+ completed ones in grey.
+As the results are produced they are listed, for each output, in the Port Results View.
+After the workflow has run (indicated by GetCitiesByCountry turning grey), you will see a string âValue 1? appear in the lower left panel. This is the identifier of the output result. If you click on this, you will see the output appear in the <em>Rendered Result</em> panel of the <em>Port Results View</em>.</p>
+<p>Congratulations, you have created and run a workflow.</p>
+<h2 id="closing-the-workflow">Closing the workflow</h2>
+<p>To close the current workflow, select <em>Close workflow</em> from the <em>File</em> menu.</p></div>
+
+ </div>
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