Java-programs require a Java Platform to run, the so-called "Java Virtual Machine" (JVM) or "Java Runtime Environment" (JRE)
It is recommended to update to the newest Java version.
You can have several Java-versions at the same time on your computer.
The JRE provides the command "java" in the bin-dirctory which is used to run strap.jar.
java -jar strap.jar
The command javaws of the Java system is used to start Java-Webstart-files
".jnlp". Java-Webstart is a
launcher for Java-programs.
The command "javaws" has 3 advantages over "java":
- The newest STRAP version is automatically downloaded.
On some Windows computers it is not easy to download files with the
ending ".jar". Java Web Start solves this problem.
- 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
Files with the ending ".jnlp" should be processed with javaws.
Web-Browser settings are usually found in the menus "Settings" or "Preferences".
See Netscape or
Step 1 firefox,
Step 2 firefox,
Step 3 firefox for how to associate javaws to
the file type ".jnlp" in the web browser.
To test whether Java-Webstart is principally working on your computer try
In case of Problems
For huge amounts of protein data increase heap memory.
Increasing memory: If you perform analyses with a large amount of
data and you get an OutOfMemoryError you need to enlarge
In case you start STRAP with Webstart please download and modify the
jnlp file. Then start the altered copy.
If you start STRAP from the command line please use the option
-Xmx256M to increase to 256Mb.
Alternatively, you can increase memory in the Java control panel.
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
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".
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 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
(16 Megabytes) and extract it on the hard disk or
By running the installer the license conditions will be displayed.
After extraction you will find three important executable files:
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.
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
which is found in
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.
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
STRAP is tested with Java version 1.5, 1.6 and 1.7 systems of Sun (Oracle) as
well as of IBM.
Back to STRAP