edit: sorry for bumping an old thread, but I believe it is better to answer than to leave open.

Reference: Problem in running Glimmer3

i dont know where to input my sequence

USAGE:  glimmer3 [options] **<sequence-file>** <icm-file> <tag>

i dont know how to build ICM

The only input needed is your genome:

long-orfs -n -t 1.15 **genome.fasta** run1.longorfs
extract -t genome.fasta run1.longorfs > run1.train
build-icm -r run1.icm < run1.train

Page 4 of Glimmer3 manual mentions the g3-from-scratch.csh script that runs the whole pipeline:

g3-from-scratch.csh genome.fasta

If these instructions are too complicated, you have to be more specific about what you tryed and the error messages thrown.