ChIPMonk - A ChIP on Chip Analysis tool
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ChIPMonk is a tool for viewing and analysing ChIP on Chip data.  It
maps one or more sets of array data onto an annotated genome assembly
and provides stastical tools to filter the data and reporting tools
to summarise it.

ChIPMonk is a cross-platform application, written in java.  In theory it
should run on any platform which has a suitable java runtime environment.
Having said that we've only tested in on Windows, MacOSX 10.4 and Linux
running the Sun v1.5 JRE.  Please let us know what happened if you try
running it on other platforms / JREs.

If you have any comments about ChIPMonk we would like to hear them.  You
can either enter them in our bug tracking system at:

http://www.bioinformatics.bbsrc.ac.uk/bugzilla/

..or send them directly to simon.andrews@bbsrc.ac.uk.


Changing Memory Limits
----------------------

ChIPMonk works with very large data sets (both genome annotations and
array data), and it therefore requires a large amount of RAM to run.

Whilst most aspects of the program can be altered from within ChIPMonk
itself, the total amount of memory available to the program is determined
when it is started.  If you want to increase the amount of memory ChIPMonk
can use you must therefore edit the startup files yourself.

Windows: On Windows ChIPMonk uses a batch file called run_chipmonk.bat
to launch the program.  This file contains the command line options which
set the amount of memory available to the program.  If you right click on 
the batch file and select edit it will be opened in an editor.  In this
file find the part which says -Xmx####m where ### is a number, and change
this to the number of Megabytes you want to make available to ChIPMonk.

OSX: ChIPMonk on OSX is distributed as an application bundle, inside which
is the configuration file which determines the amount of available memory.
To change this do the following:

1) Find the ChIPMonk application in the Finder.

2) Control-click on the application and select "Show package Contents"

3) Double click on the contents folder

4) Double click the Info.plist file (this will open an application called
Property List Editor.

5) Click the arrow next to the work Root (a series of lines should appear)

6) Click the arrow next to the word Java (another set of lines appear)

7) The last line should start with VMOptions.  At the end of this line there
should be a value which says -Xmx####m, where ### is the number of megabytes
of memory allocated to this application.  To change this double click on this
value and change that number.  Once you've finished, select File > Save to
save your changes and then quit PropertyListEditor.

8) Restart ChIPMonk and the new memory limits will be used.