The summary of tophat-cufflinks protocol is like that:

step1: generate a tophat_out folder with bam files

tophat  -G genes.gtf <index>  sample1_1.fq  sample1_2.fq    
tophat  -G genes.gtf <index>  sample2_1.fq  sample2_2.fq

step2: generate new .gtf files (assemble isoform)

cufflinks sample1/accepted_hits.bam     
cufflinks sample2/accepted_hits.bam

step3 ...

As I finally realized that, to install a rpy2 package on Windows is almost a mission impossible, I decide to install a ipython notebook server on the remote machine instead. So I can generate the R script from python and run by "R cmd run run.r". Naive, but it ...