Tophat can not find bowtie?

[qiudao]

Dear List,

I tried to use tophat for analysis of rna-seq.

However, when after I run tophat test data, it gave me the error:

./tophat -r 20 test_ref reads_1.fq reads_2.fq

Beginning TopHat run (v1.2.0)
Preparing output location ./tophat_out/
Checking for Bowtie index files
Checking for reference FASTA file
Checking for Bowtie
Error: TopHat requires Bowtie 0.12.3 or later

But I have already put the directory of "bowtie" which contains "bowtie","bowtie-build" and "bowtie-inspect" in $PATH and export it when starting the shell.

I tried two version of tophat, x86 binary and my own compiled, they gave me the same errors; I also tried two versions bowtie (0.12.5 and 0.12.7), both gave me the same error.

could someone tell me what I was missing? Thanks.

-Q