JWS-122 & JWS-116 New documentation entry with instructions on how to use the JABAWS...
authorFábio Madeira <fmmarquesmadeira@dundee.ac.uk>
Mon, 26 Jun 2017 14:49:04 +0000 (15:49 +0100)
committerFábio Madeira <fmmarquesmadeira@dundee.ac.uk>
Mon, 26 Jun 2017 14:53:16 +0000 (15:53 +0100)
30 files changed:
docs/v_2_2_0/changelog.rst
docs/v_2_2_0/docker.rst [new file with mode: 0644]
docs/v_2_2_0/getting_started.rst
docs/v_2_2_0/index.rst
website/docs/_sources/changelog.rst.txt
website/docs/_sources/docker.rst.txt [new file with mode: 0644]
website/docs/_sources/getting_started.rst.txt
website/docs/_sources/index.rst.txt
website/docs/_static/basic.css
website/docs/_static/doctools.js
website/docs/_static/pygments.css
website/docs/_static/searchtools.js
website/docs/_static/websupport.js
website/docs/advanced.html
website/docs/changelog.html
website/docs/citations.html
website/docs/client.html
website/docs/develop.html
website/docs/docker.html [new file with mode: 0644]
website/docs/genindex.html
website/docs/getting_started.html
website/docs/included_tools.html
website/docs/index.html
website/docs/jabaws_manual.pdf
website/docs/objects.inv
website/docs/search.html
website/docs/searchindex.js
website/docs/stats.html
website/docs/va.html
website/docs/war.html

index e24d5a6..cbd023a 100644 (file)
@@ -13,6 +13,7 @@ The website and documentation were improved:
 * Documentation was updated to reflect the latest changes introduced in the project.
 * Usage Statistics are now cached and refreshed every hour for improved website loading times.
 * Service Status are now similarly cached and monitored every 10 minutes.
+* We now provide a `Docker`_ image which allows for JABAWS to be run in Docker containers.
 * Downloading the JABAWS distributions no longer require 'sign in' or 'sign up' to a user account.
 * The pre-configured JABAWS Amazon Machine Image (AMI), which allowed for JABAWS to be run in the Amazon EC2 cloud, is no longer provided due to very limited use by the scientific community peers.
 
@@ -30,6 +31,7 @@ The versions of several application programs provided by JABAWS were bumped to t
 
 .. _Sphinx: http://www.sphinx-doc.org/en/stable/
 .. _AACon: http://www.compbio.dundee.ac.uk/aacon/
+.. _Docker: https://www.docker.com/
 
 ------------
 
diff --git a/docs/v_2_2_0/docker.rst b/docs/v_2_2_0/docker.rst
new file mode 100644 (file)
index 0000000..66fd290
--- /dev/null
@@ -0,0 +1,48 @@
+Docker Container
+================
+
+An alternative to running the JABAWS Virtual Appliance (VA) or the JABAWS Web Application aRchive (WAR) in your local machine, is to use `Docker`_ to handle all the requirements to deploy JABAWS in Tomcat. We provide a `Dockerfile`_, which Docker uses to build an exact image of the required system, (i.e. Apache Tomcat server with the JABAWS WAR deployed).
+
+------------
+
+.. _docker_installing:
+
+Installing Docker
+-----------------
+
+In order to run JABAWS using `Docker`_, you need docker installed and running in your system. Installation instructions are provided in the `Docker documentation pages`_.
+
+------------
+
+.. _jabaws_docker:
+
+Running JABAWS with Docker
+--------------------------
+
+Once you have docker installed and running in your machine:
+
+.. code:: bash
+
+      docker build -t jabaws:2.2 http://www.compbio.dundee.ac.uk/jabaws22/archive/docker/Dockerfile
+
+This will download the required Docker contexts (Tomcat, etc.) and setup JABAWS. Once the setup is finished you can run the JABAWS container with:
+
+
+.. code:: bash
+
+      docker run --rm -it -p 8080:8080 jabaws:2.2
+
+This will launch Tomcat and deploy JABAWS. By accessing ``localhost:8080/jabaws/`` you can verify whether the JABAWS is running properly.
+You can then use your Docker JABAWS container to power your analysis using `Jalview`_ or the `JABAWS CLI`_.
+
+
+------------
+
+.. links
+.. _Docker: https://www.docker.com/
+.. _Docker documentation pages: https://docs.docker.com/engine/installation/
+.. _JABAWS Virtual Appliance (VA): va.html
+.. _JABAWS Web Application aRchive (WAR): war.html
+.. _Dockerfile: http://www.compbio.dundee.ac.uk/jabaws22/archive/docker/Dockerfile
+.. _Jalview: getting_started.html#jalview-and-the-jabaws-public-server
+.. _JABAWS CLI: getting_started.html#command-line-client-cli
index b0d63b1..c857989 100644 (file)
@@ -7,6 +7,8 @@ JABAWS consists of a server and a client, but unlike most bioinformatics web-ser
 
 The public server based on JABAWS 2.1 at the `University of Dundee`_ has been in production since October 2013 and serviced over 442,000 jobs for users worldwide.
 
+**New:** You can now run JABAWS with `Docker`_. `Click here to learn more`_.
+
 ------------
 
 .. _benefits:
@@ -163,3 +165,5 @@ Alternatively you can use Jalview to complete the testing.
 .. _VMWare Player: http://www.vmware.com/products/player
 .. _VMWare Fusion: http://www.vmware.com/products/fusion/overview.html
 .. _VA documentation pages: va.html
+.. _Docker: https://www.docker.com/
+.. _Click here to learn more: docker.html
index 3807d9a..e61ff9b 100644 (file)
@@ -19,6 +19,7 @@ JABAWS documentation is also available in *pdf*. `Download it here`_!
    client
    war
    va
+   docker
    advanced
    develop
    stats
index e24d5a6..cbd023a 100644 (file)
@@ -13,6 +13,7 @@ The website and documentation were improved:
 * Documentation was updated to reflect the latest changes introduced in the project.
 * Usage Statistics are now cached and refreshed every hour for improved website loading times.
 * Service Status are now similarly cached and monitored every 10 minutes.
+* We now provide a `Docker`_ image which allows for JABAWS to be run in Docker containers.
 * Downloading the JABAWS distributions no longer require 'sign in' or 'sign up' to a user account.
 * The pre-configured JABAWS Amazon Machine Image (AMI), which allowed for JABAWS to be run in the Amazon EC2 cloud, is no longer provided due to very limited use by the scientific community peers.
 
@@ -30,6 +31,7 @@ The versions of several application programs provided by JABAWS were bumped to t
 
 .. _Sphinx: http://www.sphinx-doc.org/en/stable/
 .. _AACon: http://www.compbio.dundee.ac.uk/aacon/
+.. _Docker: https://www.docker.com/
 
 ------------
 
diff --git a/website/docs/_sources/docker.rst.txt b/website/docs/_sources/docker.rst.txt
new file mode 100644 (file)
index 0000000..66fd290
--- /dev/null
@@ -0,0 +1,48 @@
+Docker Container
+================
+
+An alternative to running the JABAWS Virtual Appliance (VA) or the JABAWS Web Application aRchive (WAR) in your local machine, is to use `Docker`_ to handle all the requirements to deploy JABAWS in Tomcat. We provide a `Dockerfile`_, which Docker uses to build an exact image of the required system, (i.e. Apache Tomcat server with the JABAWS WAR deployed).
+
+------------
+
+.. _docker_installing:
+
+Installing Docker
+-----------------
+
+In order to run JABAWS using `Docker`_, you need docker installed and running in your system. Installation instructions are provided in the `Docker documentation pages`_.
+
+------------
+
+.. _jabaws_docker:
+
+Running JABAWS with Docker
+--------------------------
+
+Once you have docker installed and running in your machine:
+
+.. code:: bash
+
+      docker build -t jabaws:2.2 http://www.compbio.dundee.ac.uk/jabaws22/archive/docker/Dockerfile
+
+This will download the required Docker contexts (Tomcat, etc.) and setup JABAWS. Once the setup is finished you can run the JABAWS container with:
+
+
+.. code:: bash
+
+      docker run --rm -it -p 8080:8080 jabaws:2.2
+
+This will launch Tomcat and deploy JABAWS. By accessing ``localhost:8080/jabaws/`` you can verify whether the JABAWS is running properly.
+You can then use your Docker JABAWS container to power your analysis using `Jalview`_ or the `JABAWS CLI`_.
+
+
+------------
+
+.. links
+.. _Docker: https://www.docker.com/
+.. _Docker documentation pages: https://docs.docker.com/engine/installation/
+.. _JABAWS Virtual Appliance (VA): va.html
+.. _JABAWS Web Application aRchive (WAR): war.html
+.. _Dockerfile: http://www.compbio.dundee.ac.uk/jabaws22/archive/docker/Dockerfile
+.. _Jalview: getting_started.html#jalview-and-the-jabaws-public-server
+.. _JABAWS CLI: getting_started.html#command-line-client-cli
index b0d63b1..c857989 100644 (file)
@@ -7,6 +7,8 @@ JABAWS consists of a server and a client, but unlike most bioinformatics web-ser
 
 The public server based on JABAWS 2.1 at the `University of Dundee`_ has been in production since October 2013 and serviced over 442,000 jobs for users worldwide.
 
+**New:** You can now run JABAWS with `Docker`_. `Click here to learn more`_.
+
 ------------
 
 .. _benefits:
@@ -163,3 +165,5 @@ Alternatively you can use Jalview to complete the testing.
 .. _VMWare Player: http://www.vmware.com/products/player
 .. _VMWare Fusion: http://www.vmware.com/products/fusion/overview.html
 .. _VA documentation pages: va.html
+.. _Docker: https://www.docker.com/
+.. _Click here to learn more: docker.html
index 3807d9a..e61ff9b 100644 (file)
@@ -19,6 +19,7 @@ JABAWS documentation is also available in *pdf*. `Download it here`_!
    client
    war
    va
+   docker
    advanced
    develop
    stats
index 7ed0e58..dc88b5a 100644 (file)
@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- basic theme.
  *
- * :copyright: Copyright 2007-2016 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2017 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
index 8163495..5654977 100644 (file)
@@ -4,7 +4,7 @@
  *
  * Sphinx JavaScript utilities for all documentation.
  *
- * :copyright: Copyright 2007-2016 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2017 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
index 8213e90..20c4814 100644 (file)
 .highlight .mh { color: #208050 } /* Literal.Number.Hex */
 .highlight .mi { color: #208050 } /* Literal.Number.Integer */
 .highlight .mo { color: #208050 } /* Literal.Number.Oct */
+.highlight .sa { color: #4070a0 } /* Literal.String.Affix */
 .highlight .sb { color: #4070a0 } /* Literal.String.Backtick */
 .highlight .sc { color: #4070a0 } /* Literal.String.Char */
+.highlight .dl { color: #4070a0 } /* Literal.String.Delimiter */
 .highlight .sd { color: #4070a0; font-style: italic } /* Literal.String.Doc */
 .highlight .s2 { color: #4070a0 } /* Literal.String.Double */
 .highlight .se { color: #4070a0; font-weight: bold } /* Literal.String.Escape */
@@ -59,7 +61,9 @@
 .highlight .s1 { color: #4070a0 } /* Literal.String.Single */
 .highlight .ss { color: #517918 } /* Literal.String.Symbol */
 .highlight .bp { color: #007020 } /* Name.Builtin.Pseudo */
+.highlight .fm { color: #06287e } /* Name.Function.Magic */
 .highlight .vc { color: #bb60d5 } /* Name.Variable.Class */
 .highlight .vg { color: #bb60d5 } /* Name.Variable.Global */
 .highlight .vi { color: #bb60d5 } /* Name.Variable.Instance */
+.highlight .vm { color: #bb60d5 } /* Name.Variable.Magic */
 .highlight .il { color: #208050 } /* Literal.Number.Integer.Long */
\ No newline at end of file
index bbfb3ac..c821573 100644 (file)
@@ -4,7 +4,7 @@
  *
  * Sphinx JavaScript utilities for the full-text search.
  *
- * :copyright: Copyright 2007-2016 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2017 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
index 98e7f40..53f6a45 100644 (file)
@@ -4,7 +4,7 @@
  *
  * sphinx.websupport utilities for all documentation.
  *
- * :copyright: Copyright 2007-2016 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2017 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
index 6966c9b..b11e77b 100644 (file)
@@ -37,7 +37,7 @@
         <link rel="search" title="Search" href="search.html"/>
     <link rel="top" title="JABAWS 2.2 documentation" href="index.html"/>
         <link rel="next" title="For Developers" href="develop.html"/>
-        <link rel="prev" title="Virtual Appliance (VA)" href="va.html"/> 
+        <link rel="prev" title="Docker Container" href="docker.html"/> 
 
   
   <script src="_static/js/modernizr.min.js"></script>
@@ -97,6 +97,7 @@
 <li class="toctree-l1"><a class="reference internal" href="client.html">Command Line Client (CLI)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="war.html">Web Application Archive (WAR)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="va.html">Virtual Appliance (VA)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="docker.html">Docker Container</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">Advanced Usage</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="#valid-wsdl">Valid WSDL</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#jabaws-configuration">JABAWS Configuration</a><ul>
@@ -534,7 +535,7 @@ After you have completed the editing your configuration may look like this:</p>
 </colgroup>
 <thead valign="bottom">
 <tr class="row-odd"><th class="head"><strong>Help Pages</strong></th>
-<th class="head">&nbsp;</th>
+<th class="head">&#160;</th>
 </tr>
 </thead>
 <tbody valign="top">
@@ -568,7 +569,7 @@ After you have completed the editing your configuration may look like this:</p>
         <a href="develop.html" class="btn btn-neutral float-right" title="For Developers" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
       
       
-        <a href="va.html" class="btn btn-neutral" title="Virtual Appliance (VA)" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+        <a href="docker.html" class="btn btn-neutral" title="Docker Container" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
       
     </div>
   
index b4de96b..5f51ba8 100644 (file)
@@ -96,6 +96,7 @@
 <li class="toctree-l1"><a class="reference internal" href="client.html">Command Line Client (CLI)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="war.html">Web Application Archive (WAR)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="va.html">Virtual Appliance (VA)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="docker.html">Docker Container</a></li>
 <li class="toctree-l1"><a class="reference internal" href="advanced.html">Advanced Usage</a></li>
 <li class="toctree-l1"><a class="reference internal" href="develop.html">For Developers</a></li>
 <li class="toctree-l1"><a class="reference internal" href="stats.html">Usage Statistics</a></li>
 <li>Documentation was updated to reflect the latest changes introduced in the project.</li>
 <li>Usage Statistics are now cached and refreshed every hour for improved website loading times.</li>
 <li>Service Status are now similarly cached and monitored every 10 minutes.</li>
+<li>We now provide a <a class="reference external" href="https://www.docker.com/">Docker</a> image which allows for JABAWS to be run in Docker containers.</li>
 <li>Downloading the JABAWS distributions no longer require &#8216;sign in&#8217; or &#8216;sign up&#8217; to a user account.</li>
 <li>The pre-configured JABAWS Amazon Machine Image (AMI), which allowed for JABAWS to be run in the Amazon EC2 cloud, is no longer provided due to very limited use by the scientific community peers.</li>
 </ul>
index 8b9dabc..f579a95 100644 (file)
@@ -97,6 +97,7 @@
 <li class="toctree-l1"><a class="reference internal" href="client.html">Command Line Client (CLI)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="war.html">Web Application Archive (WAR)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="va.html">Virtual Appliance (VA)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="docker.html">Docker Container</a></li>
 <li class="toctree-l1"><a class="reference internal" href="advanced.html">Advanced Usage</a></li>
 <li class="toctree-l1"><a class="reference internal" href="develop.html">For Developers</a></li>
 <li class="toctree-l1"><a class="reference internal" href="stats.html">Usage Statistics</a></li>
index 47f4574..84b2274 100644 (file)
 </li>
 <li class="toctree-l1"><a class="reference internal" href="war.html">Web Application Archive (WAR)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="va.html">Virtual Appliance (VA)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="docker.html">Docker Container</a></li>
 <li class="toctree-l1"><a class="reference internal" href="advanced.html">Advanced Usage</a></li>
 <li class="toctree-l1"><a class="reference internal" href="develop.html">For Developers</a></li>
 <li class="toctree-l1"><a class="reference internal" href="stats.html">Usage Statistics</a></li>
index 8be0fdd..17bb6a5 100644 (file)
@@ -97,6 +97,7 @@
 <li class="toctree-l1"><a class="reference internal" href="client.html">Command Line Client (CLI)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="war.html">Web Application Archive (WAR)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="va.html">Virtual Appliance (VA)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="docker.html">Docker Container</a></li>
 <li class="toctree-l1"><a class="reference internal" href="advanced.html">Advanced Usage</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">For Developers</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="#source-code">Source Code</a></li>
diff --git a/website/docs/docker.html b/website/docs/docker.html
new file mode 100644 (file)
index 0000000..d1b6809
--- /dev/null
@@ -0,0 +1,271 @@
+
+
+<!DOCTYPE html>
+<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
+<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
+<head>
+  <meta charset="utf-8">
+  
+  <meta name="viewport" content="width=device-width, initial-scale=1.0">
+  
+  <title>Docker Container &mdash; JABAWS 2.2 documentation</title>
+  
+
+  
+  
+  
+  
+
+  
+
+  
+  
+    
+
+  
+
+  
+  
+    <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
+  
+
+  
+
+  
+        <link rel="index" title="Index"
+              href="genindex.html"/>
+        <link rel="search" title="Search" href="search.html"/>
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+              <p class="caption"><span class="caption-text">Contents:</span></p>
+<ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="getting_started.html">Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="included_tools.html">Included Tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="client.html">Command Line Client (CLI)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="war.html">Web Application Archive (WAR)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="va.html">Virtual Appliance (VA)</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="#">Docker Container</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#installing-docker">Installing Docker</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#running-jabaws-with-docker">Running JABAWS with Docker</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="advanced.html">Advanced Usage</a></li>
+<li class="toctree-l1"><a class="reference internal" href="develop.html">For Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="stats.html">Usage Statistics</a></li>
+<li class="toctree-l1"><a class="reference internal" href="citations.html">Citations</a></li>
+<li class="toctree-l1"><a class="reference internal" href="changelog.html">Changelog</a></li>
+</ul>
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+      <li><a href="index.html">Docs</a> &raquo;</li>
+        
+      <li>Docker Container</li>
+    
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+            <a href="../">Return to the JABAWS homepage</a>
+          
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+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+            
+  <div class="section" id="docker-container">
+<h1>Docker Container<a class="headerlink" href="#docker-container" title="Permalink to this headline">¶</a></h1>
+<p>An alternative to running the JABAWS Virtual Appliance (VA) or the JABAWS Web Application aRchive (WAR) in your local machine, is to use <a class="reference external" href="https://www.docker.com/">Docker</a> to handle all the requirements to deploy JABAWS in Tomcat. We provide a <a class="reference external" href="http://www.compbio.dundee.ac.uk/jabaws22/archive/docker/Dockerfile">Dockerfile</a>, which Docker uses to build an exact image of the required system, (i.e. Apache Tomcat server with the JABAWS WAR deployed).</p>
+<hr class="docutils" />
+<div class="section" id="installing-docker">
+<span id="docker-installing"></span><h2>Installing Docker<a class="headerlink" href="#installing-docker" title="Permalink to this headline">¶</a></h2>
+<p>In order to run JABAWS using <a class="reference external" href="https://www.docker.com/">Docker</a>, you need docker installed and running in your system. Installation instructions are provided in the <a class="reference external" href="https://docs.docker.com/engine/installation/">Docker documentation pages</a>.</p>
+<hr class="docutils" />
+</div>
+<div class="section" id="running-jabaws-with-docker">
+<span id="jabaws-docker"></span><h2>Running JABAWS with Docker<a class="headerlink" href="#running-jabaws-with-docker" title="Permalink to this headline">¶</a></h2>
+<p>Once you have docker installed and running in your machine:</p>
+<div class="code bash highlight-default"><div class="highlight"><pre><span></span><span class="n">docker</span> <span class="n">build</span> <span class="o">-</span><span class="n">t</span> <span class="n">jabaws</span><span class="p">:</span><span class="mf">2.2</span> <span class="n">http</span><span class="p">:</span><span class="o">//</span><span class="n">www</span><span class="o">.</span><span class="n">compbio</span><span class="o">.</span><span class="n">dundee</span><span class="o">.</span><span class="n">ac</span><span class="o">.</span><span class="n">uk</span><span class="o">/</span><span class="n">jabaws22</span><span class="o">/</span><span class="n">archive</span><span class="o">/</span><span class="n">docker</span><span class="o">/</span><span class="n">Dockerfile</span>
+</pre></div>
+</div>
+<p>This will download the required Docker contexts (Tomcat, etc.) and setup JABAWS. Once the setup is finished you can run the JABAWS container with:</p>
+<div class="code bash highlight-default"><div class="highlight"><pre><span></span><span class="n">docker</span> <span class="n">run</span> <span class="o">--</span><span class="n">rm</span> <span class="o">-</span><span class="n">it</span> <span class="o">-</span><span class="n">p</span> <span class="mi">8080</span><span class="p">:</span><span class="mi">8080</span> <span class="n">jabaws</span><span class="p">:</span><span class="mf">2.2</span>
+</pre></div>
+</div>
+<p>This will launch Tomcat and deploy JABAWS. By accessing <code class="docutils literal"><span class="pre">localhost:8080/jabaws/</span></code> you can verify whether the JABAWS is running properly.
+You can then use your Docker JABAWS container to power your analysis using <a class="reference external" href="getting_started.html#jalview-and-the-jabaws-public-server">Jalview</a> or the <a class="reference external" href="getting_started.html#command-line-client-cli">JABAWS CLI</a>.</p>
+<hr class="docutils" />
+</div>
+</div>
+
+
+           </div>
+           <div class="articleComments">
+            
+           </div>
+          </div>
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+        <a href="advanced.html" class="btn btn-neutral float-right" title="Advanced Usage" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
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+      
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+  
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+  <hr/>
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+  <div role="contentinfo">
+    <p><a href="../">JABAWS 2.2</a>
+        &copy; Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Daniel Barton, Fábio Madeira, Alexey Drozdetskiy, Suzanne Duce and Geoff Barton.
+
+    </p>
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+  Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. 
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+        var DOCUMENTATION_OPTIONS = {
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+            FILE_SUFFIX:'.html',
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index a5513cc..e8eff2b 100644 (file)
@@ -96,6 +96,7 @@
 <li class="toctree-l1"><a class="reference internal" href="client.html">Command Line Client (CLI)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="war.html">Web Application Archive (WAR)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="va.html">Virtual Appliance (VA)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="docker.html">Docker Container</a></li>
 <li class="toctree-l1"><a class="reference internal" href="advanced.html">Advanced Usage</a></li>
 <li class="toctree-l1"><a class="reference internal" href="develop.html">For Developers</a></li>
 <li class="toctree-l1"><a class="reference internal" href="stats.html">Usage Statistics</a></li>
index bfa3f37..06b1f5d 100644 (file)
 <li class="toctree-l1"><a class="reference internal" href="client.html">Command Line Client (CLI)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="war.html">Web Application Archive (WAR)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="va.html">Virtual Appliance (VA)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="docker.html">Docker Container</a></li>
 <li class="toctree-l1"><a class="reference internal" href="advanced.html">Advanced Usage</a></li>
 <li class="toctree-l1"><a class="reference internal" href="develop.html">For Developers</a></li>
 <li class="toctree-l1"><a class="reference internal" href="stats.html">Usage Statistics</a></li>
 <p><em>JABAWS</em> is a collection of web services for bioinformatics, and currently provides services that make it easy to access well-known multiple sequence alignment and protein disorder prediction programs (see the list of <a class="reference external" href="included_tools.html">currently supported programs</a>). Future versions of JABAWS will incorporate other tools.</p>
 <p>JABAWS consists of a server and a client, but unlike most bioinformatics web-service systems, you can download and run both parts on your own computer! If you want a server just for yourself, then download and install the <a class="reference external" href="va.html">JABAWS Virtual Appliance (VA)</a>. It requires no configuration and is simple to install. If you want to install JABAWS for your lab or institution then download the <a class="reference external" href="war.html">JABAWS Web Application aRchive (WAR)</a>. It is slightly more complicated to configure but is very straightforward too. Finally, if you want to script against any version of JABAWS or are interested in writing your own client, the <a class="reference external" href="client.html">JABAWS Command Line Interface (CLI)</a> client is what you need.</p>
 <p>The public server based on JABAWS 2.1 at the <a class="reference external" href="http://www.compbio.dundee.ac.uk/">University of Dundee</a> has been in production since October 2013 and serviced over 442,000 jobs for users worldwide.</p>
+<p><strong>New:</strong> You can now run JABAWS with <a class="reference external" href="https://www.docker.com/">Docker</a>. <a class="reference external" href="docker.html">Click here to learn more</a>.</p>
 <hr class="docutils" />
 <div class="section" id="jabaws-benefits">
 <span id="benefits"></span><h2>JABAWS Benefits<a class="headerlink" href="#jabaws-benefits" title="Permalink to this headline">¶</a></h2>
index 5170a1f..a7ba7a5 100644 (file)
 <li class="toctree-l1"><a class="reference internal" href="client.html">Command Line Client (CLI)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="war.html">Web Application Archive (WAR)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="va.html">Virtual Appliance (VA)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="docker.html">Docker Container</a></li>
 <li class="toctree-l1"><a class="reference internal" href="advanced.html">Advanced Usage</a></li>
 <li class="toctree-l1"><a class="reference internal" href="develop.html">For Developers</a></li>
 <li class="toctree-l1"><a class="reference internal" href="stats.html">Usage Statistics</a></li>
index bc0e16c..587d388 100644 (file)
@@ -96,6 +96,7 @@
 <li class="toctree-l1"><a class="reference internal" href="client.html">Command Line Client (CLI)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="war.html">Web Application Archive (WAR)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="va.html">Virtual Appliance (VA)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="docker.html">Docker Container</a></li>
 <li class="toctree-l1"><a class="reference internal" href="advanced.html">Advanced Usage</a></li>
 <li class="toctree-l1"><a class="reference internal" href="develop.html">For Developers</a></li>
 <li class="toctree-l1"><a class="reference internal" href="stats.html">Usage Statistics</a></li>
 </li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="docker.html">Docker Container</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="docker.html#installing-docker">Installing Docker</a></li>
+<li class="toctree-l2"><a class="reference internal" href="docker.html#running-jabaws-with-docker">Running JABAWS with Docker</a></li>
+</ul>
+</li>
 <li class="toctree-l1"><a class="reference internal" href="advanced.html">Advanced Usage</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="advanced.html#valid-wsdl">Valid WSDL</a></li>
 <li class="toctree-l2"><a class="reference internal" href="advanced.html#jabaws-configuration">JABAWS Configuration</a><ul>
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@@ -95,6 +95,7 @@
 <li class="toctree-l1"><a class="reference internal" href="client.html">Command Line Client (CLI)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="war.html">Web Application Archive (WAR)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="va.html">Virtual Appliance (VA)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="docker.html">Docker Container</a></li>
 <li class="toctree-l1"><a class="reference internal" href="advanced.html">Advanced Usage</a></li>
 <li class="toctree-l1"><a class="reference internal" href="develop.html">For Developers</a></li>
 <li class="toctree-l1"><a class="reference internal" href="stats.html">Usage Statistics</a></li>
index b975f05..5fb8ea2 100644 (file)
@@ -1 +1 @@
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celist:4,sequenceutil:4,sequenti:4,serial:4,serv:[0,4,11],server:[3,4,5,8,10,11],server_url:0,servic:[0,1,2,3,6,8,9,10,11],servicenam:[0,3],servicestatu:0,servlet:[1,11],set:[0,3,4,9,10,11],setenv:0,setexecflag:[0,4],setexecutableflag:4,setnativespecif:0,setup:[5,6],setvalu:4,seven:4,sever:[0,1,4,6],sftp:10,sge:0,sge_root:0,sgpgeadarlrafahaqgvdaqrlvfmpklphpqylaryrhadlfldthpynahttasdalwtgc:4,share:11,shell:10,sherstnev:2,ship:6,shot:10,should:[0,1,4,6,9,10,11],show:[3,9],shown:[3,6],side:4,sign:[1,3],signific:0,silent:4,similar:[4,10],similarli:[1,10],simpl:[0,4,6],simplest:9,simpli:[0,4,6,10,11],simplifi:[0,1],sinc:[0,4,6,11],singl:[6,10,11],site:[3,11],six:4,size:[6,8,9],skeletalexecut:4,sleep:4,slightli:6,small:[0,11],smaller:0,soap:[0,3,4,6],softwar:[3,4,6],some:[0,1,4],someth:4,sometim:[4,9,11],soon:9,sourc:[0,3,6,8,11],space:[4,11],special:4,specif:[0,3,4,11],specifi:[0,3,9],speed:[0,4],sphinx:1,split:4,src:[0,4,6],ssh:10,stabil:4,stage:4,stand:6,standalon:10,standard:[0,1,4,9],standlon:10,start:[0,8,9,10],startup:0,stat:9,statist:[0,1,4,8],statpag:[0,4],statu:[0,1,6,8],step:0,still:11,stlhdvtalghlatakhirhhgidllfdlrgwggggrpevfalrpapvqvnwlaypgtsgapwmd:4,stop:1,storag:0,store:[0,4],stori:9,straight:0,straightforward:6,stream:9,string:[1,4],structur:[0,1,2,8],stub:4,subfold:4,submiss:0,submit:[0,4,6,9],substitut:0,successfulli:0,suffici:[4,10,11],suffix:0,suggest:[0,4],suit:[0,4,6,10],suitabl:0,summari:9,sun:[0,4,11],suppli:[0,1,4,11],support:[0,1,3,4,6,10,11],sure:[0,4,9,11],swap:1,symbol:[0,1,9],system:[4,5,6,8,9,10,11],tabl:[0,9],take:[0,4,10],task:[0,4,6,10,11],tcoffeew:[0,3],tell:0,temp:4,templat:8,temporari:[0,4,9],ten:4,tend:4,termin:0,test:[3,6,8,10,11],testcas:4,testng:4,testoutput:0,testsrc:4,text:[4,9],than:[0,1,4,10,11],thei:[0,4,6,10],them:[0,3,4,6,10,11],thi:[0,1,3,4,5,6,8,9,10,11],thin:4,third:[4,11],though:4,thread:[0,1,4,11],three:[0,4],through:[4,6],thu:[0,4],thw:0,time:[0,1,4,9,10],timestamp:9,tip:0,titl:9,tmp:0,togeth:[3,4],tomcat:[0,1,5,6,8,10,11],tomcat_dir:0,tomcat_root:[0,9],tomcatroot:11,too:[0,6,11],tool:[0,4,6,8,10],top:4,tostr:4,total:9,trace:0,tracker:[4,8],treat:0,trim:3,troshin:2,troubleshoot:8,tune:10,turnkei:[6,10],tvalfealqrrqpdlqmhlfatsgddgstlrtrlaqastlhdvtalghlatakhirhhgidllfd:4,two:[0,1,4,11],txt:[0,4,9],type:[0,4,6],uncom:0,undeploi:11,undeploy:11,under:[0,4,6],underneath:4,uniqu:9,unit:8,univers:[0,4,6],unix:[6,9],unless:10,unlik:[6,10],unpack:[6,10,11],unsupportedruntimeexcept:4,until:[0,4],updat:[0,1,4],upon:[0,4],upper:4,url:[0,3,4,6,10,11],us_intl:10,usag:[1,8],use:[0,1,2,3,4,5,6,9,10,11],used:[0,1,3,4,10,11],useful:[0,3,4],user:[0,1,6,9,10,11],usernam:9,uses:[0,4,5,6,10,11],using:[0,3,4,5,6,9,11],utf:[9,11],util:[0,4],valid:8,valu:[0,3,4],valv:0,variabl:[4,8],variou:0,veri:[0,1,4,6],verifi:5,version:[0,3,6,7,8,9,10,11],vgavepfaflsedasaaeqlacartraqaiaasvrplaptrvrskgplrvgfvsngfgahptgl:4,via:[3,6,10],viennarna:7,view:[4,8],violat:4,virtial:10,virtual:[0,5,8,9],virtualbox:[1,10],visial:0,visit:6,visual:[1,9],visualis:9,vm_ip:10,vmdk:10,vmware:[1,6,10],vmx:10,vrwtqqrhaeaavllqqasdaapehpgialwlghaledagqaeaaaaaytrahqllpeepyitaq:4,vwmare:10,wai:[0,3,4,6,9,10],wait:[0,4],want:[0,3,4,6,8,10],war:[1,4,5,8,9,10],warn:0,wast:0,watch:4,web:[0,1,2,3,5,8,10],webal:0,webapp:[0,6,11],webapplicationpath:0,webmean:10,webservic:[0,4,6],websit:[1,4],weight:4,welcom:3,well:[0,4,6,11],were:[1,4,9,11],what:[0,6,10],whatev:[0,4],when:[0,2,9,10],whenev:4,where:[0,3,4,6,9,10],wherea:0,whether:[4,5,9,10],which:[0,1,3,4,5,6,9,10,11],who:[0,4,6,10],whole:[0,9],whose:9,why:0,wide:6,window:[0,4,6,10,11],wish:0,within:[0,1,4,9],without:[0,4,10,11],work:[2,4,6,8,10,11],worldwid:6,would:[0,3,4,6,10],wrap:4,wrapper:4,write:[3,6,8],writeclustalalign:4,written:0,wrongparameterexcept:4,wsbuild:4,wsdl:[4,8],wsimport:[0,4],www:[0,4,5,11],x86:[0,11],xincgc:0,xml:[0,4,9,11],xms512m:0,xmx1024m:0,xxx:0,xxxlimit:0,xxxparamet:[0,4],xxxpreset:0,yesterdai:3,you:[0,2,3,4,5,6,8,9,10,11],your:[3,5,6,8,9,10,11],your_jaba_context_nam:0,your_jabaws_server_url:0,yourself:[0,6],yvlgdafalppalepfysehvlrlqgafqpsdtsrvvaeppsrtqcglpeqgvvlccfnnsykln:4,zip:11},titles:["Advanced Usage","Changelog","Citations","Command Line Client (CLI)","For Developers","Docker Container","Getting Started","Included Tools","Welcome to JABAWS&#8217;s documentation!","Usage Statistics","Virtual Appliance (VA)","Web Application Archive (WAR)"],titleterms:{"16th":1,"1st":1,"2nd":1,"function":4,"new":4,"public":6,Adding:4,For:4,The:4,accept:0,access:[4,9],acid:7,advanc:0,align:[4,7],amino:7,analyt:0,api:4,applianc:[6,10],applic:[6,9,11],archiv:[6,11],artifact:4,balanc:0,benefit:6,binari:0,brief:4,build:4,calcul:4,changelog:1,check:4,citat:2,cli:[3,6],client:[3,4,6],cluster:0,code:4,command:[3,4,6],compil:0,complet:4,configur:[0,9,10],connect:4,conserv:7,contain:5,content:[0,9],custom:4,dec:1,defin:0,detail:9,develop:4,directori:9,disord:7,distribut:[4,6],docker:5,document:8,engin:0,environ:0,exampl:[3,4],execut:[0,9],file:[0,4],from:4,get:6,googl:0,guid:4,includ:7,instal:[3,5,10,11],intern:0,jabaw:[0,4,5,6,8,9,10],jalview:6,job:[0,9],jul:1,june:1,limit:0,line:[3,4,6],list:9,load:0,local:0,log:0,mafft:0,multipl:7,obtain:0,oct:1,overview:4,paramet:4,pre:0,predict:7,prepar:4,preset:4,privileg:9,program:4,project:4,protein:7,recompil:0,releas:1,request:0,reus:0,rna:7,run:5,secondari:7,sequenc:[4,7],server:[0,6,9],servic:4,size:0,sourc:4,start:6,statist:9,statu:4,structur:[4,7],system:0,templat:4,test:[0,4],tomcat:9,tool:7,troubleshoot:11,unit:4,usag:[0,3,9,10,11],valid:0,variabl:0,version:1,view:9,virtual:[6,10],war:[0,6,11],web:[4,6,9,11],welcom:8,work:0,write:4,wsdl:0,your:[0,4]}})
\ No newline at end of file
index 40e0f84..6276852 100644 (file)
@@ -97,6 +97,7 @@
 <li class="toctree-l1"><a class="reference internal" href="client.html">Command Line Client (CLI)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="war.html">Web Application Archive (WAR)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="va.html">Virtual Appliance (VA)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="docker.html">Docker Container</a></li>
 <li class="toctree-l1"><a class="reference internal" href="advanced.html">Advanced Usage</a></li>
 <li class="toctree-l1"><a class="reference internal" href="develop.html">For Developers</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">Usage Statistics</a><ul>
 <div class="highlight-bash"><div class="highlight"><pre><span></span><span class="c1"># Enable/disable cluster statistics collector true = enable, false = disable</span>
 cluster.stat.collector.enable<span class="o">=</span><span class="nb">false</span>
 <span class="c1"># Maximum amount of time the job is considered be running in hours. Optional defaults to 7 days (168h)</span>
-cluster.stat.maxruntime<span class="o">=</span>24
+cluster.stat.maxruntime<span class="o">=</span><span class="m">24</span>
 </pre></div>
 </div>
 <div class="highlight-bash"><div class="highlight"><pre><span></span><span class="c1"># Enable/disable cluster statistics collector true = enable, false = disable</span>
 local.stat.collector.enable<span class="o">=</span><span class="nb">true</span>
 <span class="c1"># Maximum amount of time the job is considered to be running in hours. Optional defaults to 24 hours</span>
-local.stat.maxruntime<span class="o">=</span>6
+local.stat.maxruntime<span class="o">=</span><span class="m">6</span>
 </pre></div>
 </div>
 <p>If the statistics collector is enabled then the crawler starts automatically soon after (10 minutes for local engine, and 60 minutes for cluster engine) the JABAWS web application and will be collecting the execution statistics every 24 hours after the start.</p>
index 97b595b..273ea4a 100644 (file)
@@ -36,7 +36,7 @@
               href="genindex.html"/>
         <link rel="search" title="Search" href="search.html"/>
     <link rel="top" title="JABAWS 2.2 documentation" href="index.html"/>
-        <link rel="next" title="Advanced Usage" href="advanced.html"/>
+        <link rel="next" title="Docker Container" href="docker.html"/>
         <link rel="prev" title="Web Application Archive (WAR)" href="war.html"/> 
 
   
 </li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="docker.html">Docker Container</a></li>
 <li class="toctree-l1"><a class="reference internal" href="advanced.html">Advanced Usage</a></li>
 <li class="toctree-l1"><a class="reference internal" href="develop.html">For Developers</a></li>
 <li class="toctree-l1"><a class="reference internal" href="stats.html">Usage Statistics</a></li>
   
     <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
       
-        <a href="advanced.html" class="btn btn-neutral float-right" title="Advanced Usage" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
+        <a href="docker.html" class="btn btn-neutral float-right" title="Docker Container" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
       
       
         <a href="war.html" class="btn btn-neutral" title="Web Application Archive (WAR)" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
index 9ad9a91..7a95950 100644 (file)
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="va.html">Virtual Appliance (VA)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="docker.html">Docker Container</a></li>
 <li class="toctree-l1"><a class="reference internal" href="advanced.html">Advanced Usage</a></li>
 <li class="toctree-l1"><a class="reference internal" href="develop.html">For Developers</a></li>
 <li class="toctree-l1"><a class="reference internal" href="stats.html">Usage Statistics</a></li>