Running Geneset enrichment analysis on commandline

java -cp /stor1/shah/Ruben_peptide/gsea_analysis/gsea2-2.06.jar
-Xmx2000m xtools.gsea.Gsea
-res foo_expression_values.gct
-cls foo_expression_values.cls#Normal_versus_Treatment
-gmx msigdb.v2.5.symbols.gmt -chip HG_U133_Plus_2.chip
-collapse true -mode Max_probe -norm meandiv -nperm 1000
-permute phenotype -rnd_type no_balance -scoring_scheme weighted
-rpt_label my_analysis -metric Signal2Noise -sort real -order descending -include_only_symbols true -make_sets true -median false -num 100
-plot_top_x 20 -rnd_seed timestamp -save_rnd_lists false -set_max 500 -set_min 15 -zip_report false -out /stor1/shah/Ruben_peptide/gsea_analysis -gui false

commandline for GSEA.