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 on the cloud, for one or many users | +JABAWS on the Amazon cloud |
| Running JABAWS for my group, lab, or organization on the local infrastructure | -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 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 (this is optional if you use 32 bit version of Linux): -
- If you are on Linux or Mac (OSX intel Mac only)
- cd to webapps/jabaws/binaries/src/ and execute ./setexecflag.sh script to ensure the JABAWS binaries can be executed.
- - If you are on 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. -
- cd to webapps/jabaws/binaries/src/ and execute ./setexecflag.sh script. -
- Download the JABAWS WAR file +
- Download and install Apache-Tomcat.
+ You will need at least Tomcat version 5.5 of (we would recommend version 7.0) and at least Java 1.6 (i.e. JAVA 6). +
+ - 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). +
- 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 several ways.
-
-
- Visit Services Status page available from the main menu using your web browser. +
- 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 @@ -104,12 +105,10 @@