From b895c8df3e237da572dc256cb5f8d4d1f3e58f8a Mon Sep 17 00:00:00 2001 From: Sasha Sherstnev Date: Fri, 13 Jun 2014 07:06:17 +0100 Subject: [PATCH] Replace temporary path to the download app with the standard one --- website/contacts.html | 2 +- website/index.html | 16 ++++++++-------- website/jabaws_funding.html | 2 +- website/man_about.html | 4 ++-- website/man_client.html | 2 +- website/man_dev.html | 10 +++------- website/manual_qs_amazon.html | 2 +- website/manual_qs_client.html | 4 ++-- website/manual_qs_va.html | 4 ++-- website/manual_qs_war.html | 4 ++-- website/quick_start.html | 2 +- 11 files changed, 24 insertions(+), 28 deletions(-) diff --git a/website/contacts.html b/website/contacts.html index 7cf944a..c46fc4f 100644 --- a/website/contacts.html +++ b/website/contacts.html @@ -29,7 +29,7 @@ Home Getting Started Manual - Download + Download Usage Statistics Services Status Contact Us diff --git a/website/index.html b/website/index.html index 86d5f94..d600183 100644 --- a/website/index.html +++ b/website/index.html @@ -28,7 +28,7 @@ Home Getting Started Manual - Download + Download Usage Statistics Services Status Contact Us @@ -79,7 +79,7 @@ computing resources.

For Users

- The Server: JABAWS Virtual Appliance: (440M) + The Server: JABAWS Virtual Appliance: (440M) or JABAWS on Amazon Webservices Cloud
The Main Client: Jalview (18M)

To use JABAWS web services on most operating systems, just download and install @@ -94,7 +94,7 @@ computing resources.

For System Administrators

- The Server: JABAWS Web + The Server: JABAWS Web Application aRchive (55M)

JABAWS requires a Servlet 2.4 compatible servlet container like Apache Tomcat @@ -107,11 +107,11 @@ computing resources.

For Bioinformaticians/Developers

-The Server: JABAWS Web Application aRchive (55M) +The Server: JABAWS Web Application aRchive (55M)
The Client: - Command Line Client binary | source + Command Line Client binary | source

You can either use the JABAWS Virtual Appliance or the JABAWS Web Application aRchive (WAR) from your own computer or a lab server. @@ -126,7 +126,7 @@ Check out the quick start guide for furt

Public JABAWS Server

-

You can access our public JABAWS web services with our command line client, +

You can access our public JABAWS web services with our command line client, Jalview, or with your own program. Jalview version 2.8 or later is fully compatible with JABAWS 2.1. The latest versions of Jalview are configured to use public JABAWS server by default.

    @@ -137,7 +137,7 @@ title="http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?" rel=

These web services accept submissions of less than one thousand sequences. Should you find this to be insufficient for your needs, or if you are concerned about privacy or on an unreliable network connection, then you can - download and run the JABAWS Server on your own hardware.

+ download and run the JABAWS Server on your own hardware.

diff --git a/website/jabaws_funding.html b/website/jabaws_funding.html index dd850b9..be90e0e 100644 --- a/website/jabaws_funding.html +++ b/website/jabaws_funding.html @@ -28,7 +28,7 @@ Home Getting Started Manual - Download + Download Usage Statistics Services Status Contact Us diff --git a/website/man_about.html b/website/man_about.html index 4965ffb..95b0f35 100644 --- a/website/man_about.html +++ b/website/man_about.html @@ -132,7 +132,7 @@
  • RNAalifold from ViennaRNA (2.0)
    • -All these codes including Jronn and AAcon are available at the Download +All these codes including Jronn and AAcon are available at the Download section (registration is required). @@ -214,7 +214,7 @@ section (registration is required). JABAWS web services are WS-I basic profile compliant, which means they can be accessed using any programming language or system that can utilize standard SOAP web services. The WSDL for each service is published on the JABAWS home page, and you can use this to automatically generate service bindings for your program. If you use Java - you may wish to use our client package to access JABAWS. + you may wish to use our client package to access JABAWS. This package is based on the autogenerated source code produced by wsimport, which is the Java tool for creating web service bindings. In addition, this offers some additional methods that simplify working with JABAWS. For more information please refer to the data model javadoc. diff --git a/website/man_client.html b/website/man_client.html index 585cb17..757f672 100644 --- a/website/man_client.html +++ b/website/man_client.html @@ -53,7 +53,7 @@

    JABAWS Command Line Client Usage

    -The command line client comes as a part of client package which you are welcome to download. +The command line client comes as a part of client package which you are welcome to download. The command line client can be used to align sequences using any of JABAWS supported web services. The client is OS independent and supports most of the functions which can be accessed programmatically via JABAWS API. Using this client you could align sequences using presets or custom parameters, please see examples of this below. Here is the list of options supported by the command line client. diff --git a/website/man_dev.html b/website/man_dev.html index de5c544..35da5fd 100644 --- a/website/man_dev.html +++ b/website/man_dev.html @@ -111,13 +111,9 @@

    Connecting to JABAWS

    For a complete working example of JABAWS command line client please see compbio.ws.client.Jws2Client class. JABAWS command line client -<<<<<<< HEAD -source code is available from the download page. Please note that for now all +source code is available from the download page. Please note that for now all the examples are in Java other languages will follow given a sufficient demand.

    -======= -source code is available from the download page. Please note that for now all -the examples are in Java, other languages will follow if there is sufficient demand.

    ->>>>>>> 42a3637e24a7a65b5a1e6048e581df998b4a4f95 +

    Download a binary JABAWS client. Add the client to the class path. The following code excerpt will connect your program to Clustal web service deployed in the University of Dundee.

    @@ -272,7 +268,7 @@ one of the Clustal web service presets. There is also a JABAWS binary client. +JABAWS binary client. Please make sure that the client is in the Java class path before running this example.

     import java.io.ByteArrayInputStream;
diff --git a/website/manual_qs_amazon.html b/website/manual_qs_amazon.html
index ea250a7..03cf6fb 100644
--- a/website/manual_qs_amazon.html
+++ b/website/manual_qs_amazon.html
@@ -28,7 +28,7 @@
 	Home 
 	Getting Started 
 	Manual 
-	Download 
+	Download 
 	Usage Statistics
 	Services Status
 	Contact Us
diff --git a/website/manual_qs_client.html b/website/manual_qs_client.html
index 8f496ed..afb97c0 100644
--- a/website/manual_qs_client.html
+++ b/website/manual_qs_client.html
@@ -28,7 +28,7 @@
 	Home 
 	Getting Started 
 	Manual 
-	Download 
+	Download 
 	Usage Statistics
 	Services Status
 	Contact Us
@@ -66,7 +66,7 @@
 
 
 
    The JABAWS command line client
    
-