From: Fábio Madeira <fmmarquesmadeira@dundee.ac.uk>
Date: Fri, 19 May 2017 16:55:58 +0000 (+0100)
Subject: JWS-116 Some minor fixes to the documentation pages and added the alignment image... 
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=75d370a35bde9ed74bcc45d7582ed02bd048ef24;p=jabaws.git

JWS-116 Some minor fixes to the documentation pages and added the alignment image to the getting started pages.
---

diff --git a/docs/v_2_2_0/getting_started.rst b/docs/v_2_2_0/getting_started.rst
index 3d22148..4b02327 100644
--- a/docs/v_2_2_0/getting_started.rst
+++ b/docs/v_2_2_0/getting_started.rst
@@ -5,6 +5,7 @@ Getting Started
 
 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 `JABAWS Virtual Appliance (VA)`_. 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 (WAR)`_. 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 Interface (CLI)`_ client is what you need.
 
+The public server based on JABAWS 2.0 at the `University of Dundee`_ has been in production since November 2013 and serviced over 430,000 jobs for users worldwide.
 
 ------------
 
@@ -29,7 +30,7 @@ JABAWS Benefits
 JABAWS Distributions
 --------------------
 
-.. tip:: To help you choose the JABAWS distribution that better suits your needs and read on the quickstart guides below.
+.. tip:: To help you choose the JABAWS distribution that better suits your needs read on the quickstart guides below.
 
 **I want to use JABAWS for...**
 
@@ -48,6 +49,12 @@ Jalview and the JABAWS Public Server
 
 `Jalview`_, a multiple sequence alignment and analysis application, is a good example of a graphical JABAWS client. This client uses the same functionality as the `JABAWS Command Line Interface (CLI)`_ client, but instead allows JABAWS services to be accessed in a more user-friendly manner, through a graphical user interface. In this way, this is the easiest way to run JABAWS web services. Simply launch `Jalview`_ and run any of the methods provided under the 'Web Service' menu. Jalview uses the public JABAWS server by default. If you are concerned about privacy or want to run sensitive analysis on your own hardware, you can either setup a local `JABAWS Virtual Appliance (VA)`_ or configure the `JABAWS Web Application aRchive (WAR)`_ in your infrastructure.
 
+.. image:: ../../website/static/img/aligment.png
+   :height: 318
+   :width: 608
+   :scale: 100 %
+   :align: left
+
 ------------
 
 .. _jabaws-cli:
diff --git a/website/docs/v_2_2_0/_images/aligment.png b/website/docs/v_2_2_0/_images/aligment.png
new file mode 100644
index 0000000..863745b
Binary files /dev/null and b/website/docs/v_2_2_0/_images/aligment.png differ
diff --git a/website/docs/v_2_2_0/_sources/getting_started.rst.txt b/website/docs/v_2_2_0/_sources/getting_started.rst.txt
index 3d22148..4b02327 100644
--- a/website/docs/v_2_2_0/_sources/getting_started.rst.txt
+++ b/website/docs/v_2_2_0/_sources/getting_started.rst.txt
@@ -5,6 +5,7 @@ Getting Started
 
 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 `JABAWS Virtual Appliance (VA)`_. 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 (WAR)`_. 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 Interface (CLI)`_ client is what you need.
 
+The public server based on JABAWS 2.0 at the `University of Dundee`_ has been in production since November 2013 and serviced over 430,000 jobs for users worldwide.
 
 ------------
 
@@ -29,7 +30,7 @@ JABAWS Benefits
 JABAWS Distributions
 --------------------
 
-.. tip:: To help you choose the JABAWS distribution that better suits your needs and read on the quickstart guides below.
+.. tip:: To help you choose the JABAWS distribution that better suits your needs read on the quickstart guides below.
 
 **I want to use JABAWS for...**
 
@@ -48,6 +49,12 @@ Jalview and the JABAWS Public Server
 
 `Jalview`_, a multiple sequence alignment and analysis application, is a good example of a graphical JABAWS client. This client uses the same functionality as the `JABAWS Command Line Interface (CLI)`_ client, but instead allows JABAWS services to be accessed in a more user-friendly manner, through a graphical user interface. In this way, this is the easiest way to run JABAWS web services. Simply launch `Jalview`_ and run any of the methods provided under the 'Web Service' menu. Jalview uses the public JABAWS server by default. If you are concerned about privacy or want to run sensitive analysis on your own hardware, you can either setup a local `JABAWS Virtual Appliance (VA)`_ or configure the `JABAWS Web Application aRchive (WAR)`_ in your infrastructure.
 
+.. image:: ../../website/static/img/aligment.png
+   :height: 318
+   :width: 608
+   :scale: 100 %
+   :align: left
+
 ------------
 
 .. _jabaws-cli:
diff --git a/website/docs/v_2_2_0/getting_started.html b/website/docs/v_2_2_0/getting_started.html
index 23b2ff0..ddd25b4 100644
--- a/website/docs/v_2_2_0/getting_started.html
+++ b/website/docs/v_2_2_0/getting_started.html
@@ -180,6 +180,7 @@
 <h1>Getting Started<a class="headerlink" href="#getting-started" title="Permalink to this headline">¶</a></h1>
 <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 2.0 at the <a class="reference external" href="http://www.compbio.dundee.ac.uk/">University of Dundee</a> has been in production since November 2013 and serviced over 430,000 jobs for users worldwide.</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>
@@ -198,7 +199,7 @@
 <span id="distributions"></span><h2>JABAWS Distributions<a class="headerlink" href="#jabaws-distributions" title="Permalink to this headline">¶</a></h2>
 <div class="admonition tip">
 <p class="first admonition-title">Tip</p>
-<p class="last">To help you choose the JABAWS distribution that better suits your needs and read on the quickstart guides below.</p>
+<p class="last">To help you choose the JABAWS distribution that better suits your needs read on the quickstart guides below.</p>
 </div>
 <p><strong>I want to use JABAWS for...</strong></p>
 <ul class="simple">
@@ -211,6 +212,7 @@
 <div class="section" id="jalview-and-the-jabaws-public-server">
 <span id="jabaws-jalview-public"></span><h3>Jalview and the JABAWS Public Server<a class="headerlink" href="#jalview-and-the-jabaws-public-server" title="Permalink to this headline">¶</a></h3>
 <p><a class="reference external" href="http://www.jalview.org/">Jalview</a>, a multiple sequence alignment and analysis application, is a good example of a graphical JABAWS client. This client uses the same functionality as the <a class="reference external" href="client.html">JABAWS Command Line Interface (CLI)</a> client, but instead allows JABAWS services to be accessed in a more user-friendly manner, through a graphical user interface. In this way, this is the easiest way to run JABAWS web services. Simply launch <a class="reference external" href="http://www.jalview.org/">Jalview</a> and run any of the methods provided under the &#8216;Web Service&#8217; menu. Jalview uses the public JABAWS server by default. If you are concerned about privacy or want to run sensitive analysis on your own hardware, you can either setup a local <a class="reference external" href="va.html">JABAWS Virtual Appliance (VA)</a> or configure the <a class="reference external" href="war.html">JABAWS Web Application aRchive (WAR)</a> in your infrastructure.</p>
+<a class="reference internal image-reference" href="_images/aligment.png"><img alt="_images/aligment.png" class="align-left" src="_images/aligment.png" style="width: 608.0px; height: 318.0px;" /></a>
 <hr class="docutils" />
 </div>
 <div class="section" id="command-line-client-cli">
diff --git a/website/docs/v_2_2_0/jabaws_manual.pdf b/website/docs/v_2_2_0/jabaws_manual.pdf
index abed494..1090697 100644
Binary files a/website/docs/v_2_2_0/jabaws_manual.pdf and b/website/docs/v_2_2_0/jabaws_manual.pdf differ
diff --git a/website/docs/v_2_2_0/searchindex.js b/website/docs/v_2_2_0/searchindex.js
index 1554e06..d8cbd6a 100644
--- a/website/docs/v_2_2_0/searchindex.js
+++ b/website/docs/v_2_2_0/searchindex.js
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