Prerequisites
The CG-CAT toolsuite is written in Java and need at least Java Version 6
or newer installed on your system. Java is available for most common
systems from different vendors. CG-CAT toolsuite was tested with
Oracle Java
and OpenJDK.
Startup instructions
The Java archive itself contains both tools (r2cat and treecat). Assuming
the downloaded archive is in the current directory you can start r2cat with
java -Xmx1024M -cp r2cat.jar de.bielefeld.uni.cebitec.r2cat.R2cat
and treecat with
java -Xmx1024M -cp r2cat.jar de.bielefeld.uni.cebitec.treecat.Treecat
on command line. If you want to match larger sequences, increase
the -Xmx memory parameter.
Attention! To use more than 4 Gb you need a
64 Bit capable system and you may also add -d64
as startup argument (depending on OS).
In case of problems running a tool from the Contig Arragement Toolsuite
from command line feel free to contact
us. CG-CAT is licenced under GPL
licence and also available from GitHub.
