• About
• bioshell.bioinformatics
• bioshell.biosimulations
• bioshell.experimental
• Examples gallery
• Download
• Servers
• Blog
• Forum

Install BioShell

Do you have JAVA?

/usr/java/jdk1.5.0_06/jre

. If not, you can do it on your account, e.g. in

/home/john/bin/jre

. Remember to edit your

.bashrc

or

.bash_profile

script and add JAVA

bin

directory to your PATH shell variable:

PATH=$PATH:/usr/java/jdk1.5.0_06/jre/bin

or:

PATH=$PATH:/home/john/bin/jdk1.5.0_06/jre/bin

depending on where you have installed JRE.

Installing BioShell toolkit

Download BioShell distribution:

then simply copy the downloaded files to the directory of your choice, e.g. to /home/john/bin/BioShell:

When the destination directory contains jbcl and monomers libraries, you have also to set up CLASSPATH shell variable, by adding the following line to your startup script. For example, if your shell is bash, add them to .bashrc. The file names added to CLASSPATH must be of course as the files in your local directory.

CLASSPATH=$CLASSPATH:/home/john/bin/BioShell/jbcl-2.1.jar: \  /home/john/bin/BioShell/monomers-2.1.jarexport CLASSPATH

Now you can use all BioShell command-line tools: Strc, StrCalc, Seq, Clust, RmsCalc or Trac. Just type: java RmsCalc to see command-line help for a given program (in this case RmsCalc)).

BioShell scripting library

Jython

With the new BioShell distribution it is possible to access all its objects from a (more or less) Python level. What does it mean? Well, it can be python, although implemented in java. This tool is called Jython and can be obtained from its website. Download an installer class (currently the newest version is jython_installer-2.2.1.jar) and launch it - usually double click should work. If not try:

java -jar jython_installer-2.2.1.jar 

(Click on the screenshots below to enlarge)

	Select your favorite language (English or German) and click next
	Mark "I accept" and click next
	Choose the installation directory and click next
	Choose the JAVA directory. The installer will give you a hint. Then click next
	Look on the settings one again and click next. After one or two "next" buttons it will be finished.

To make you life easier you may add Jython to your PATH variable. Now you can type jython to get a console that behaves as a regular Python would. At first run, Jython will look for all jar files on your classpath which may take a while. Finally you can try to type some Python commands at Jython prompt:

>>> print 'hello world',1+1*(3-1) hello world 3

BioShell scripts

In your scripts run by Jython you can use Python syntax and BioShell packages as Python modules. For a test, put the following code in a bioshell_info.py file:

from jbcl.util import JBCLInfo info = JBCLInfo.getInfo() print "This BioShell installation is based on",     info.getSVNVersion() ," SVN snapshot" print "Last compilation on:",     info.getSVNTime()

Once you execute the script by typing jython bioshell_info.py you should get an output similar to the following:

This BioShell installation is based on 497  SVN snapshot Last compilation on: 2007-10-30 23:18:42 -0400 (Tue, 30 Oct 2007)

It is also a good idea to start a Jython script from the following line:

#!/bin/env jython

for example:

#!/bin/env jython  from jbcl.util import JBCLInfo  info = JBCLInfo.getInfo() print "This BioShell installation is based on", \     info.getSVNVersion() ," SVN snapshot" print "Last compilation on:", \     info.getSVNTime()

Then, if you make your script executable, you won't need to invoke Jyton. Just to type:

./bioshell_info.py

OutOfMemoryError in JAVA

Sometimes your command (either execution of BioShell application or a jython script) may end up with the following message:

Exception in thread "main" java.lang.OutOfMemoryError: Java heap space

This is because all java applications (in particular Jython, which is a Python interpreter written in JAVA) are executed in a sandbox, called JAVA virtual machine (JVM). For security reasons, JVM limits the amount of RAM that any application may allocate. If your program exceeds this limit, it will be killed. You can however adjust the limit by yourself. In the case of command-line BioShell programs, simply start typing your Trac command with:

java -Xmx1000m Trac

where -Xmx1024m sets up one gigabyte (1024Mb) memory limit for Trac application

In the case of Jython scritps the solution is more tricky. First, you have to find your jython executable. This is a quite short text file that looks more or less as below:

#!/bin/sh  # This file was generated by the Jython installer # Created on Wed Nov 07 11:52:40 EST 2007 by john  CP="/home/john/bin/jython/jython.jar" if [ ! -z "$CLASSPATH" ] then   CP=$CP:$CLASSPATH fi "/home/john/bin/jdk1.6.0_02/jre/bin/java" -Dpython.home="/home/john/bin/jython" \         -classpath "$CP" org.python.util.jython "$@"

The only thing you must change is to add -Xmx1024m in the last line of this script. After that the whole script should look as follows:

#!/bin/sh  # This file was generated by the Jython installer # Created on Wed Nov 07 11:52:40 EST 2007 by john  CP="/home/john/bin/jython/jython.jar" if [ ! -z "$CLASSPATH" ] then   CP=$CP:$CLASSPATH fi "/home/john/bin/jdk1.6.0_02/jre/bin/java" \         -Xmx1500m -Dpython.home="/home/john/bin/jython" \         -classpath "$CP" org.python.util.jython "$@"

Useful links

The following sites may be useful in learning python:

• Python official site: www.python.org
• Jython official site: www.jython.org
• Dave Kuhlman's Jython tutorial is available here
• "Dive Into Python" - excellent free book introducing into Python programming, available also in Polish from here.
• "Python 2.4 Quick Reference".
• BioShell API documentation and example scripts