From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Mon, 1 Jul 2013 14:14:16 +0000 (+0100)
Subject: Merge branches 'JABAWS_Release_2_1' and 'JABAWS_Release_2_1' of https://source.jalvie... 
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=5e7cd807ed94d8e176375f183430ae3977825876;p=jabaws.git

Merge branches 'JABAWS_Release_2_1' and 'JABAWS_Release_2_1' of https://source.jalview.org/git/jabaws into JABAWS_Release_2_1

Conflicts:
	website/man_about.html
Tweaked the wording a bit more - introduced standard man_about.html#jabaX.Y.Z style name anchor for update history
---

5e7cd807ed94d8e176375f183430ae3977825876
diff --cc website/index.html
index ee35139,c60ab98..532c5d1
--- a/website/index.html
+++ b/website/index.html
@@@ -114,13 -115,13 +114,11 @@@ title="http://www.compbio.dundee.ac.uk/
     or if you are concerned about privacy or on an unreliable network connection, then you can 
     <a href="http://www.compbio.dundee.ac.uk/download">download</a> and run the JABAWS Server on your own hardware.</p>
  <h3>Previous versions of JABAWS </h3>
- <p>Old JABAWS versions are available here:
-   <strong><a href="http://www.compbio.dundee.ac.uk/jabaws1">http://www.compbio.dundee.ac.uk/jabaws1</a> and 
-   <a href="http://www.compbio.dundee.ac.uk/jabaws2">http://www.compbio.dundee.ac.uk/jabaws2</a></strong>. 
-   We advise you to update to the JABAWS 2.0.1 as this version is fully backward compatible with JABAWS v1.0 and v2.0 and 
-   contain  numerous improvements. Please consult the <a href="man_about.html#jalviewsup">manual</a> for more information 
-   on compatibility between versions.
- </p>
 -<p>Old JABAWS version is available here:
 -  <strong><a href="http://www.compbio.dundee.ac.uk/jabaws1">http://www.compbio.dundee.ac.uk/jabaws1</a> and 
 -  <a href="http://www.compbio.dundee.ac.uk/jabaws2">http://www.compbio.dundee.ac.uk/jabaws2</a></strong>. 
 -  We advise you to update to the JABAWS 2.0.1 as this version is fully backward compatible with JABAWS v1.0 and v2.0 and 
 -  contain  numerous improvements. Please consult the <a href="man_about.html#jalviewsup">manual</a> for more information 
 -  on versions compatibility.
 -</p>
++<p>We advise you to update to JABAWS 2.0.1 as this version is fully backward compatible with JABAWS v1.0 and v2.0 and 
++  contains <a href="man_about.html#jaba2.0.1">some important bug fixes</a>. Please consult the <a href="man_about.html#jalviewsup">manual</a> for more information 
++  on compatibility between versions.</p><p>Should you require them, however, old versions of JABAWS are available here:</p><ul><li>
++  <strong><a href="http://www.compbio.dundee.ac.uk/jabaws1">http://www.compbio.dundee.ac.uk/jabaws1</a></strong></li> 
++  <li><strong><a href="http://www.compbio.dundee.ac.uk/jabaws2">http://www.compbio.dundee.ac.uk/jabaws2</a></strong></li></ul> 
  <h3>Reference</h3>
  <p><span class="hightlight">
  </span> Peter V. Troshin, James B. Procter and Geoffrey J. Barton - &quot;Java Bioinformatics Analysis Web Services for 
diff --cc website/man_about.html
index 20c6a22,1f55cbc..f0c9b53
--- a/website/man_about.html
+++ b/website/man_about.html
@@@ -79,20 -80,23 +79,22 @@@
    Virtual Appliance. It requires no configuration and is simple to install. If you want to install JABAWS for your 
    lab or institution then download the JABAWS Web Application aRchive. 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 JABAWS command line client is what you need. </p>
+   in writing your own client, the JABAWS command line client is what you need.
+ </p>
+ 
  <h3><a name="wjaba" id="wjaba"></a>JABAWS Benefits</h3>
  <ul>
 -  <li>Can be deployed on most operating systems, as a VMware or other compatible Virtual Appliance or a Tomcat Java Web Application.</li>
 -  <li>Comes complete with sources and binaries for all the bioinformatics programs that it runs.</li>
 -  <li>Can operate as a stand alone server or one that submits jobs to a cluster <em>via</em> <a href="http://www.drmaa.org/">DRMAA</a>.</li>
 -  <li>Easy to access from <a href="http://www.jalview.org">Jalview</a> using its graphical client, or using the JABAWS command line client.</li>
 -  <li>Clients can submit jobs to any JABAWS servers that you might want to access, such as the one running on your local computer, 
 -      your lab's server, or the publicly available services at the <a href="http://www.compbio.dundee.ac.uk/">University of Dundee</a>.</li>
 -  <li>Local or intranet installation eliminates any security concerns you might have about sending sensitive data over the internet.</li>
 -  <li>Wide range of configuration options to control size of jobs accepted by a server and the command line options available for the program run by a service.</li>
 +<li>Can be deployed on most operating systems, as a VMware or other compatible Virtual Appliance or a Tomcat Java Web Application.</li>
 +<li>Comes complete with sources and binaries for all the bioinformatics programs that it runs.</li>
 +<li>Can operate as a stand alone server or one that submits jobs to a cluster <em>via</em> <a href="http://www.drmaa.org/">DRMAA</a>.</li>
 +<li>Easy to access from <a href="http://www.jalview.org">Jalview</a> using its graphical client, or using the JABAWS command line client.</li>
 +<li>Clients can submit jobs to any JABAWS servers that you might want to access, such as the one running on your local computer, 
 +    your lab's server, or the publicly available services at the <a href="http://www.compbio.dundee.ac.uk/">University of Dundee</a>.</li>
 +<li>Local or intranet installation eliminates any security concerns you might have about sending sensitive data over the internet.</li>
 +<li>Wide range of configuration options to control size of jobs accepted by a server and the command line options available for the program run by a service.</li>
  </ul>
 -
  <h3><a name="alprog" id="alprog"/>JABA Web Services Programs </h3>
 -<p>JABAWS currently provides access to the following programs:</p>
 +<p> JABAWS currently provides access to the following programs:</p>
  <p>Multiple Sequence Alignement </p>
  <ul>
    <li><a href="http://www.clustal.org/omega">Clustal Omega </a> (version 1.0.2)</li>
@@@ -114,23 -118,20 +116,33 @@@
  <ul>
    <li><span style="color:black; font-weight:normal; text-align:left;"><a href="http://www.compbio.dundee.ac.uk/aacon">AACon</a></span> (1.0) </li>
    </ul>
- <h3><a name="jaba2"></a>What is new in JABAWS 2.0.1? </h3>
- <p>Compared to JABAWS 1, JABAWS 2.0.1 offers a greater number and diversity of web services, Amazon EC2 integration and improved easy of use. It contains </p>
 -
 -<h3><a name="jaba2"></a>What is new in JABAWS 2.0.1? </h3>
 -<p>This release of JABAWS 2.0.1 is mostly bug fixing release. This is a list of bugs which have been fixed in JABAWS 2.0.1:</p>
++<h3><a name="jaba2.0.1"/></a>What is new in JABAWS 2.0.1? </h3>
++<p>JABAWS Version 2.0.1 includes several minor updates and bug fixes for <a href="#jaba2">JABAWS Version 2</a>. These are listed below:</p>
+ <ul>
+   <li>Disembl returned swapped strings for HOTLOOPS and REM465</li>
+   <li>Jronn failed to process jobs with more than 3 sequences</li>
 -  <li>JABAWS could not deal with FASTA records with the '&gt' symbols in the record identificator</li>
++  <li>JABAWS could not deal with FASTA records with '&gt' symbols in the record identificator</li>
+   <li>Change of parameter description for AAcon: parameters have been replaced with options for calculation methods. This allows a user to get several AAcon's conservation scores 
+       in one call</li>
+   <li>JABAW never cleaned up job directories. Now JABAWS deletes the job directory if it exist longer then a period defined in Engine.properties</li>
+   <li>Default web security has been incompatible with Tomcat 7.0.31 and newer</li>
+   </ul>
++  <a name="jaba2"/><strong>JABAWS Version 2 (Released 16th Dec 2011)</strong><p>Compared to JABAWS 1, JABAWS 2 offers a greater number and diversity of web services, Amazon EC2 integration and improved ease of use.</p><p>It contains:</p>
 +<ul><li>updates for all multiple sequence alignment services</li>
 +  <li>four new protein disorder prediction services</li>
 +  <li>Clustal Omega multiple sequence alignment web service</li>
 +  <li>amino acid conservation service</li>
 +  <li>web services execution statistics visualization </li>
-   <li>web services  status check from a web page</li>
++  <li>web services status check from a web page</li>
 +  <li>VirtualBox support was dropped in favour of VMware</li>
 +  <li>new WAR package for Mac users</li>
 +  <li>Amazon Machine Image (AMI) distributive to enable users to use JABAWS on the EC2 cloud</li>
 +  <li>Improved web services client API</li>
 +  <li>Simplified WAR package installation</li>
 +  </ul>
  
  <h3><a name="jabaclient" id="jabaclient"></a>What is JABAWS client?</h3>
 +
  <p>
    A JABAWS client is a program that lets you run the bioinformatics methods for which a JABAWS server provides web 
    services. The most basic JABAWS client is a command line Java application which can call any of the JABAWS web