Java Bioinformatics Analysis Web Services (JABAWS) download -page

JABAWS Server Virtual Appliance

JABAWS virtual machine is a way of running fully functional JABA Web Services on your own computer. To use virtual machine (VM) you have to install a software for running it. We would recommend VMWare Player for Windows and Linux users or VMware Fusion for Mac users. Jalview can use your local JABAWS VA.

JABAWS Virtual Appliance: download (520M)

Please check out our manual for the detailed instructions.

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JABAWS Server Web Application

The JABAWS Server Web Application aRchive (WAR) version is for you if you want to deploy JABAWS for many users e.g. your laboratory or if you are an expert user and want to have more control on JABAWS. You can also use this version for Mac and Linux computers if you do not want to use virtualization. Finally, you can use this version with a cluster.
- The server is provided as a self-contained Web Application - aRchive (WAR) containing all necessary binaries. WAR file can be deployed on any - web application server - - supporting at the Java servlet specification v. 2.4 or above, i.e. Tomcat 7.0.

A JABAWS WAR for all platforms (comes with precompiled Linux x86 and Windows binaries): download -(55M)
A JABAWS WAR for Mac (comes with precompiled Mac binaries): download (51M)

- - -

Please bear in mind that if you deploy JABAWS WAR on Windows, not all web services will be functional. Use the JABAWS Server VA package instead. - -

- -

JABAWS Command Line Client

The command line client is an executable Java program for scripting against JABA web services. Its also useful as an example of how to access JABAWS services if you intend to use JABAWS in your own program, with functions demonstrating how to discover command line parameters and presets supported by a service, and how to run, monitor and retrieve the results of a job. Note: The client is used in the Jalview 2.6.1 source code to autogenerate a graphical user interface for JABA services.

Command line client -
- binaries: download (80 K)
- source: download (70 K)
-

The command line client will display help documentation if it is run with no arguments, the same information is also given in the command line client's manual page.

Version

Current JABAWS version is 2.0 release date 15 August 2011.

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The Complete Source Code

If you want to add another web service or modify JABAWS in any way just download a complete JABAWS source code. We offer the code under Apache licence. The code archive contains the complete Eclipse JABAWS project, but Eclipse is not - necessary to build it. Please examine the Ant build file (build.xml) - to build and test JABAWS from sources.

A complete Eclipse project package: download (82M)
JABAWS source only package: download (250K)

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- -

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 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.

Usage: java -jar <path_to_jar_file> -h=host_and_context -s=serviceName ACTION [OPTIONS]
-h=<host_and_context> - a full URL to the JABAWS web server including context path e.g. http://10.31.10.159:8080/ws
-s=<ServiceName> - one of [MafftWS, MuscleWS, ClustalWS, ClustalOWS, TcoffeeWS, ProbconsWS, AAConWS, JronnWS, DisemblWS, GlobPlotWS, IUPredWS] diff --git a/website/man_configuration.html b/website/man_configuration.html index b401c8c..f5348ec 100644 --- a/website/man_configuration.html +++ b/website/man_configuration.html @@ -39,7 +39,7 @@ JABAWS JABAWS Development -Download +Download Usage Statistics Services Status Contact Us diff --git a/website/man_dev.html b/website/man_dev.html index 0831503..f541bd4 100644 --- a/website/man_dev.html +++ b/website/man_dev.html @@ -39,7 +39,7 @@ JABAWS JABAWS Development -Download +Download Usage Statistics Services Status Contact Us @@ -107,7 +107,7 @@

Additional utility libraries this client depend upon is the compbio-util-1.3.jar and compbio-annotation-1.0.jar.
Please refer to a data model javadoc for a detailed description of each class and its methods.

Connecting to JABAWS

For a complete working example of JABAWS command line client please see compbio.ws.client.Jws2Client class. JABAWS command line client 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.

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.

import java.net.URL;
import javax.xml.namespace.QName;
@@ -214,7 +214,7 @@ FileOutputStream outStream = new FileOutputStream(file);
ClustalAlignmentUtil.writeClustalAlignment(outStream, align);

A complete client example

Finally, a complete example of the program that connects to JABAWS Clustal service and aligns sequences using one of the Clustal web service preset. Three is also a PDF version of this example with syntax highlighted. The text comments are commented by block style comments e.g. /* comment */, the alternatives given in the code are line commented // comment. You may want to remove line style comments to test alternatives of the functions. All you need for this to work is a JABAWS binary client. Please make sure that the client is in the Java class path before running this example.

 import java.io.ByteArrayInputStream;
 import java.io.FileNotFoundException;
diff --git a/website/man_server_dev.html b/website/man_server_dev.html
index f1196f0..3edfaa2 100644
--- a/website/man_server_dev.html
+++ b/website/man_server_dev.html
@@ -38,7 +38,7 @@
 		JABAWS	
 		JABAWS Development
 	
-Download 
+Download 
 Usage Statistics
  Services Status
 Contact Us
diff --git a/website/man_servervm.html b/website/man_servervm.html
index 234f426..d2001f6 100644
--- a/website/man_servervm.html
+++ b/website/man_servervm.html
@@ -39,7 +39,7 @@
 		JABAWS	
 		JABAWS Development
 	
-Download 
+Download 
 Usage Statistics
  Services Status
 Contact Us
diff --git a/website/man_serverwar.html b/website/man_serverwar.html
index f50e8c5..76c58f5 100644
--- a/website/man_serverwar.html
+++ b/website/man_serverwar.html
@@ -39,7 +39,7 @@
 		JABAWS	
 		JABAWS Development
 	
-Download 
+Download 
 Usage Statistics
  Services Status
 Contact Us
diff --git a/website/man_stats.html b/website/man_stats.html
index 4e12de7..487aa13 100644
--- a/website/man_stats.html
+++ b/website/man_stats.html
@@ -39,7 +39,7 @@
 		JABAWS	
 		JABAWS Development
 	
-Download 
+Download 
 Usage Statistics
  Services Status
 Contact Us
diff --git a/website/manual_qs_client.html b/website/manual_qs_client.html
index 9c07636..49c926c 100644
--- a/website/manual_qs_client.html
+++ b/website/manual_qs_client.html
@@ -24,7 +24,7 @@
 Home
     Getting Started 
     Manual 
-	Download
+	Download
     Usage Statistics
 	 Services Status
 	Contact Us
@@ -67,7 +67,7 @@
 
 The JABAWS command line client

 Download the Client Jar (80 K)
+"http://www.compbio.dundee.ac.uk/download/get?id=min-jaba-client-2.0.jar">Download the Client Jar (80 K)
 
 This is a single java archive which contains the JABAWS command line client. 
 It requires Java version 1.6 to run, and allows anyone who wants to connect 
diff --git a/website/manual_qs_va.html b/website/manual_qs_va.html
index 7d706fc..cdae95a 100644
--- a/website/manual_qs_va.html
+++ b/website/manual_qs_va.html
@@ -24,7 +24,7 @@
 Home
     Getting Started 
     Manual 
-	Download
+	Download
     Usage Statistics
 	 Services Status
 	Contact Us
@@ -61,7 +61,7 @@
 
 
 
Running JABAWS on your local machine

-  Download JABAWS Virtual Appliance (520M) 
+  Download JABAWS Virtual Appliance (520M) 
 
 The Virtual Appliance (VA) package allows you to run a JABAWS server installed on TurnKey Linux as a virtual machine on your laptop or desktop computer. A complete guide to the JABAWS VA is given in the manual, but for the impatient, a brief instructions are given below:
 
diff --git a/website/manual_qs_war.html b/website/manual_qs_war.html
index 78503b5..e3c0cc8 100644
--- a/website/manual_qs_war.html
+++ b/website/manual_qs_war.html
@@ -25,7 +25,7 @@
 Home
     Getting Started 
     Manual 
-	Download
+	Download
     Usage Statistics
 	 Services Status
 	Contact Us
@@ -69,7 +69,7 @@
 
This is for anyone who wants to run JABAWS for their group, lab or organization, or wants to enable their local JABA server to use the cluster or perform very large tasks.
 
 
-Download the JABAWS WAR for your platform 
+Download the JABAWS WAR for your platform 
   Download and install Apache-Tomcat.

    You will need at least version 5.5 of Tomcat (we would recommend version 7.0) and at least version 1.6 (i.e. JAVA 6) of Java.
   Drop the JABAWS WAR file into tomcat/webapps directory.
diff --git a/website/quick_start.html b/website/quick_start.html
index 34ec930..415ab93 100644
--- a/website/quick_start.html
+++ b/website/quick_start.html
@@ -24,7 +24,7 @@
 	Home
     Getting Started 
     Manual 
-	Download
+	Download
     Usage Statistics
 	Services Status
 	Contact Us
-- 
1.7.10.2

JABAWS Server Virtual Appliance

JABAWS Server Web Application

JABAWS Command Line Client

Version

The Complete Source Code

For Users

For System Administrators

For Bioinformaticians/Developers

Public JABAWS Server

Reference

JABAWS MANUAL

JABAWS Command Line Client Usage

Connecting to JABAWS

A complete client example

The JABAWS command line client

Running JABAWS on your local machine