BIRCH - Pre-installation steps

Create a separate account for the BIRCH Administrator

BIRCH is deliberately designed so that the BIRCH Administrator does not need root privileges. Even if the person who administers BIRCH has root access, there should be a separate user account for the BIRCH Administrator. This limits the severity of potential mistakes made by the BIRCH administrator. As well, if BIRCH files and directories belonged to root, the severity of potential security holes would be far greater than if they are owned by a regular user account.

Ask your system administrator to create a separate account for administering the BIRCH system. For example, the userid might be 'birch' and the home directory might be '/home/birch'. This account is simply a regular user account with no special privileges. If administration of BIRCH is to be shared among several people, it may be good to also create a group called 'birch', to which all BIRCH administrators belong.

Hardware

The current BIRCH release needs about 500 Mb of disk space, not counting space for optional databases.
Platforms currently supported:

solaris-sparc
solaris-amd64
linux-intel
linux-x86_64

Minimal CPU/RAM - BIRCH installs and runs well even on fairly slow, older machines eg.

Sun Ultra 60 (2 x 360 Mhz; 512 Mb RAM)
Intel Pentium II (1 x 400 Mhz; 384 Mb RAM)

Tools and libraries

Required

Python 2.2 or later (required for some system administration scripts)

standard in most Linux and Solaris distributions

http://www.python.org/
The 'python' command must be in the users' $path. Test python by typing 'python -V' at the command line. If Python is installed, the -V option will print out the version of python eg.
```
Python 2.3.3
```
Java 1.4.2 or later (required for Java applications and for installation)

standard on Solaris.

http://java.sun.com/j2se/
Test java by typing 'java -version' at the command line. If Java is installed and present in the system $PATH, you should get a message like
```
java version "1.5.0_07"
Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_07-b03)
Java HotSpot(TM) Server VM (build 1.5.0_07-b03, mixed mode)
```
If you get this message, no further steps are necessary.

On the other hand, if you get a 'Command not found' message, or a message like this
```
java version "1.4.2"
gij (GNU libgcj) version 4.1.1 20060525 (Red Hat 4.1.1-1)

Copyright (C) 2006 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
```
either Java is not on your system, or is not in the search path. gij is NOT Java! For full instructions on setting up Java on your system, inst.java.html.

/bin/csh
Surprisingly, some systems (eg. Mandrake) do NOT have a /bin/csh, by default. This is odd, since it greatly limits compatability other Unix systems. In any case, at least some Mandrake systems do not have csh, or even tcsh, by default. To find out whether or not you have csh, type 'which csh'. If you don't have csh, tcsh is a good substitute (which tcsh). If you have neither of the two, I suggest installing tcsh, which will be on your original installation disks, or may need to be downloaded. Once tcsh is installed in /bin, do the following:

cd /bin
ln -s tcsh csh

This command creates a symbolic link called 'csh', which points to tcsh. Now, when a csh script executes, it will be run by tcsh. tcsh has replaced csh on most recent Unix and Linux systems.

Optional

The TIGR Microarray programs, MIDAS and MEV will run without Java3D, but certain analytical methods such as Principal Component Analysis require Java3D.

Please send suggestions of comments regarding this page to frist@cc.umanitoba.ca