Tophat mean inner distance error for SOLID data

[repinementer]

Sorry I solved the above question.
Now I'm unable to detect bowtie, the same old error.
I learnt setting up path for tophat and bowtie previously and successfully installed and worked with them for few months.
Now I installed new updated versions and did the same set up. This time bow tie is not detecting.
Any suggestions.

tophat -r 20 test_ref reads_1.fq reads_2.fq

[Fri Oct 29 11:33:47 2010] Beginning TopHat run (v1.1.2)
-----------------------------------------------
[Fri Oct 29 11:33:47 2010] Preparing output location ./tophat_out/
[Fri Oct 29 11:33:48 2010] Checking for Bowtie index files
[Fri Oct 29 11:33:48 2010] Checking for reference FASTA file
[Fri Oct 29 11:33:48 2010] Checking for Bowtie
	Bowtie version:			 0.12.7.0
[Fri Oct 29 11:33:48 2010] Checking for Samtools
	[FAILED]
Error: bowtie not found on this system

bashrc profile

cat .bashrc 
# .bashrc

# Source global definitions
if [ -f /etc/bashrc ]; then
	. /etc/bashrc
fi
#export PATH=$PATH:/home/choijk/Gireesh/tophat-1.0.13/bin 
#export PATH=$PATH:/home/choijk/Gireesh/bowtie-0.11.3 
export PATH=$PATH:/home/choijk/Gireesh/sofware/bowtie-0.12.7
export PATH=$PATH:/home/choijk/Gireesh/sofware/tophat-1.1.2/bin 
# User specific aliases and functions

Versions checked

$ bowtie-build --version
bowtie-build version 0.12.7
64-bit
Built on sycamore.umiacs.umd.edu
Tue Sep 7 17:19:06 EDT 2010
#####################
$ tophat -v
TopHat v1.1.2

Any suggestions?