the ‘new’ error message refers to a nonexistant Cairo library on your system, which is needed for the AnnotationSketch component of GenomeTools. If you do not need this, do a ‘make cleanup’ and recompile with the additional make option ‘cairo=no’, e.g. ‘make errorcheck=no cairo=no’. This will disable support for AnnotationSketch and remove the cairo [...]]]>

the ‘new’ error message refers to a nonexistant Cairo library on your system, which is needed for the AnnotationSketch component of GenomeTools. If you do not need this, do a ‘make cleanup’ and recompile with the additional make option ‘cairo=no’, e.g. ‘make errorcheck=no cairo=no’. This will disable support for AnnotationSketch and remove the cairo dependency.

As for your other question, you can use the ‘gt suffixerator’ tool as described. However, the ‘gt’ binary is placed in the ‘bin/’ subdirectory of your GenomeTools source directory after compiling. Please keep that in mind and call ‘bin/gt’ if necessary.
You should be able to run the command line exactly as described if you install the ‘gt’ binary system-wide (‘make install’) or add its location to your PATH environment variable.

First, we should also install ruby  and cairo separately !