Java Basics

      java -jar strap.jar
    

      javaws  http://www.bioinformatics.org/strap/strap.jnlp
    

1. The newest STRAP version is automatically downloaded.
2. On some Windows computers it is not easy to download files with the ending ".jar". Java Web Start solves this problem.
3. Some users are within an Intranet and reach the Internet with a proxy-server. If this is the case Java Web Start may be able to automatically obtain the proxy-settings from the Web-Browser.

Web-Browser settings

Demos

In case of Problems

• Try with a different Web Browser. On Windows try the IE.
• Install the newest Java again.
• Clear cache: Java remembers all downloaded files in cache. It might be necessary to clear the cache, either with the Java-control panel or at the command line shell:

  javaws -uninstall

• In rare cases there can be an error message

  Splash:   sysCreateListenerSocket failed:

  when the javaws-command shown above is run in the terminal shell.
  One reason might be that Loopback device is not up. Check Localhost with ping:

  ping 127.0.0.1

  If not then switch it on. On UNIX/LINUX enter the command in a root shell:

  /sbin/ifconfig lo 127.0.0.1 up

  Also the additional option for javaws -Xnosplash can help (see ): Create a shell script JavawsNoSplash.bat with the content:

  javaws -Xnosplash   $*

  Asterisk-dollar is a place-holder for all program parameters. On Windows the "$*" by "%*". On all other OS make the file executable for example with the command "chmod a+x JavawsNoSplash.bat". Tell the browser to open jnlp with this file instead of directly calling javaws.
• For solving Web-proxy problems, a good idea is to remove the file ~/.java/deployment/deployment.properties and to enter the network proxy settings again with the Control-Panel.
• Still not working: In case that all computers in the Intranet contact the Internet via a Proxy Server, the proxy can be set in the Java Control Panel. On Windows the Control Panel is found in Windows_key>Settings>Java. On Linux start "ControlPanel" which is in the bin-directory of Java.

OS-specific

Windows     Macintosh Unix/Linux    

Java control panel

The Java control panel is found in the Windows-Menu/Settings/Java. In the control panel the Web-proxy can be specified.

Installation without Administrator rights

If you are not a previledged user you can still install java. Before you start please agree to the terms of use of the JRE by the Sun. Unzip the file http://www.bioinformatics.org/strap/dataFiles/jre1.6.0.zip to your hard-disk or USB-stick. Then find the program \bin\javaws.exe in the extracted files. Tell your browser to use it for jnlp-files.

Starting Java programs from command-line

If starting STRAP with Javaws fails, it is worth trying to download and start strap.jar by double click. If this also fails try to start STRAP from the command-shell because this allows to observe possible error messages. For this purpose download strap.jar to the folder "C:\temp". You need to open a command-shell (MS-DOS-shell) by chosing "Run program" and typing "cmd".

        C:
        cd \temp
        java.exe -jar strap.jar
      

If it tells "java.exe: command not found" you must search for "java.exe" on your hard disk and enter the full path like:

C:\programs\jre1.6.0_02\bin\java.exe -jar strap.jar

Debian: Debian or Debian based systems like Ubuntu provide the Java package openjdk. Java can be installed with the following shell command:

        sudo apt-get install openjdk
      

Or it may be

        sudo apt-get install openjdk-6-jre
      

On all (other) Linux systems Java can be installed in the following way wheras no changes to the system are necessary and other existing Java installations are not touched. Administration previledges are not required: Download the self-extracting archive Java (16 Megabytes) and extract it on the hard disk or an USB-stick.

        mkdir /local/java
        sh path/jre-XXX-linux-i586.bin 
      

By running the installer the license conditions will be displayed. After extraction you will find three important executable files:

        /local/java/jreXXX/bin/java
        /local/java/jreXXX/bin/javaws
        /local/java/jreXXX/bin/ControlPanel
      

The command java is used to start jar-files with the ending ".jar". This requires the option -jar:

        
        /local/java/jreXXX/bin/java -jar strap.jar
      

The second command javaws is used to start Java-Webstart-files with the ending ".jnlp". Java-Webstart is a launcher for Java-programs which takes care that outdated files are automatically updated. Always the newest program version is started. The web browser must be told the complete path /local/java/jreXXX/bin/javaws.

        /local/java/jreXXX/bin/javaws  http://www.bioinformatics.org/strap/strap.jnlp
      

The following is to run applets in Firefox. It is not required for STRAP.

        ln -s  /local/java/jreXXX/plugin/i386/ns7/libjavaplugin_oji.so  ~/.mozilla/plugins/
      

Setting up the Browser

Usually, nothing needs to be set up. The web browser should process the file strap2.jnlp with the program javaws which is found in /Applications/utilities/java. Otherwise see Browser settings.

GUI in STRAP

Some short cuts are X-Windows like and not Mac-like, as they work with the CTRL instead of the command key. The right mouse button brings up a . CTRL+ALT simulates the right mouse button in case the mouse has only one button. Multiple selections: CTRL + Left-click or SHIFT + Left-click.

Compilers

The compilers for standard computer languages are usually not installed on Macintosh computers but can be installed from the system DVD by the user. The compilers (f77, c++ and cc) are part of the Xcode package. The advantage of having these compilers is that all embedded Bioinformatics programs in STRAP can be used. Only a minimal set of Bioinformatics programs in STRAP are precompiled for PPC. For Intel Macintosh computers, Bioinformatics programs installed from source code will run faster because an Intel specific executable is built instead of using the PPC version. After installing the compilers you should remove the entire directory

        rm -r ~/.StrapAlign/bin 
      

to force STRAP to install all external programs again.