You can submit a tophat job in batch mode with the following command:
bsub [LSF options] "tophat [tophat options] <genome_index_base> <reads1_1[,...,readsN_1]> [reads1_2,...readsN_2]"
Here you need to replace [tophat options] with tophat command line options (please run tophat -h for getting a list of all command line options) and [LSF options] with LSF parameters for the resource requirements of the job. Please find a documentation about the parameters of bsub on the wiki page about the batch system. Please have a look at https://ccb.jhu.edu/software/tophat/manual.shtml for more information about the input files (<genome_index_base> <reads1_1[,...,readsN_1]> [reads1_2,...readsN_2]) that are required for running tophat.