Installing CGAT


AlignmentViewer is written in Java and should run on any machine supporting Java (JDK 1.4 or higher).

DataServer is a set of Perl scripts and assumes Unix environment with Perl installed (version 5.8 or higher). It also assumes that the perl executable is installed in the /usr/bin directory; please make a symbolic link if it is located in a different directory. The LWP (libwww-perl) module, which is downloadable from the CPAN site, is also required when you want to download data from the MBGD server. DataServer also needs an HTTPD server for communicating with the client program. In this manual, we assume that Apache HTTPD version 2.0 or more is installed on your server machine.

CGAT uses several programs for calculating alignments of two sequences and identifying several feature segments on individual sequences. Currently the following programs are supported:

You should install one or more of the above programs on the server machine before installing the CGAT DataServer. Please refer to the above URL for installing individual programs. Basically, the DataServer assumes at least the NCBI Blast/MegaBlast package is installed.