Getting Started
-Choose a JABAWS distribution
-| I want to use JABAWS for... | Quick Guide | ||
|---|---|---|---|
| Running Muptiple Sequence Alignments through Jalview on my own computer | -JABAWS Virtual Appliance (VA) | +Running Muptiple Sequence Alignments through Jalview on my own computer | +JABAWS Virtual Appliance (VA) | +
| Running JABAWS on the cloud, for one or many users | +JABAWS on the Amazon cloud | ||
| Running JABAWS for my group, lab, or organization | -JABAWS Web Application aRchive (WAR) | +Running JABAWS for my group, lab, or organization on the local infrastructure | +JABAWS Web Application aRchive (WAR) |
| Accessing a JABAWS server from my own code | -JABAWS Java Client | +Accessing a JABAWS server from my own code | +JABAWS Java Client |
Installing A JABAWS Server Web Application Archive (WAR) package
- -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.
++ 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 with all binaries (45M) -
- Download and install Apache-Tomcat.
- You will need at least version 5.5 of Tomcat (we would recommend version 6.0) and at least version 1.6 (i.e. JAVA 6) of Java.
+ - 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.
- (Re)start the Tomcat.
- Once the tomcat has started, it should automatically unpack the WAR into the webapps directory (if it doesn't, then you'll need to do this manually, it's just a zip archive in the end). -
- You then need to complete the installation of the executable binaries: -
- If you are on Linux
cd to webapps/jabaws/binaries/src/ and execute ./setexecflag.sh script to ensure the JABAWS binaries can be executed.
- - If you are on a Mac (OSX intel mac only) or other unix-like architecture with gnu compilers available: -
- cd to webapps/jabaws/binaries/src/ and execute ./compilebin.sh script to compile all binaries JABAWS depends on. -
- cd to webapps/jabaws/binaries/src/ and execute ./setexecflag.sh script. -
- If you are on Mac or other unix-like architecture with GNU compilers available or you'd like to get a maximum performance +
- cd to webapps/jabaws/binaries/src/ and execute ./compilebin.sh script to compile all binaries JABAWS depends on. +
Testing
-You can test that your JABAWS server is working in two ways.
+You can test that your JABAWS server is working in several ways.
-
+
- Visit Services Status page available from the JABAWS main page using your web browser. +
- If you are working on the command line, then use the command line client shipped with the JABAWS war to test it by running: -java -jar <Path to tomcat WebApp directory>/jabaws/WEB-INF/lib/jaba-client.jar -h http://localhost:8080/jabaws -In this example we assumed that your JABAWS server URL is http://localhost:8080 and JABAWS context path is jabaws + java -jar <Path to tomcat WebApp directory>/jabaws/WEB-INF/lib/jaba-client.jar -h=http://localhost:8080/jabaws + In this example we assumed that your JABAWS server URL is http://localhost:8080 and JABAWS context path is jabaws -
- Alternately, you can point Jalview at your new server:
- Launch the desktop version of Jalview @@ -96,12 +99,10 @@ In this example we assumed that your JABAWS server URL is Last update: 1 April 2011
-Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK