Tophat2 can't find Bowtie2

[rnavon]

Hi Everyone,

After my previous installed tophat/bowtie versions worked without a problem, I wanted to update to the newest versions and also installed tophat2 and bowtie2. Both programs have links to them from the /bin directory which is in the path.
When trying to run the running example, tophat2 claims I do not have the correct version of bowtie installed. I'm a UNIX newbie and would appreciate any help and ideas!

Thanks!

[galaxy01@gene3 test_data]$ 
[galaxy01@gene3 test_data]$ bowtie --version
bowtie version 0.12.5
64-bit
Built on sycamore.umiacs.umd.edu
Sat Apr 24 15:56:29 EDT 2010
Compiler: gcc version 4.1.2 20080704 (Red Hat 4.1.2-46)
Options: -O3 -m64  -Wl,--hash-style=both
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}
[galaxy01@gene3 test_data]$ 
[galaxy01@gene3 test_data]$ 
[galaxy01@gene3 test_data]$ bowtie2 --version
/bin/bowtie2-align version 2.1.0
64-bit
Built on igm3
Thu Feb 21 09:33:38 EST 2013
Compiler: gcc version 4.5.4 (GCC) 
Options: -O3 -m64 -msse2 -funroll-loops -g3 
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}
[galaxy01@gene3 test_data]$ 
[galaxy01@gene3 test_data]$ 
[galaxy01@gene3 test_data]$ tophat2 --version
TopHat v2.0.7
[galaxy01@gene3 test_data]$ 
[galaxy01@gene3 test_data]$ 
[galaxy01@gene3 test_data]$ tophat2 test_ref reads_1.fq reads_2.fq

[2013-02-26 09:35:20] Beginning TopHat run (v2.0.7)
-----------------------------------------------
[2013-02-26 09:35:20] Checking for Bowtie
Error: TopHat requires Bowtie 2.0.5 or later
[galaxy01@gene3 test_data]$

[GenoMax]

Can you unlink (or rename) bowtie (v.1) in /bin temporarily to see if that allows TopHat to recognize the correct version it needs?

[rnavon]

I'll try that but it's not a permanent solution as I want to be able to keep the previous version for other users.
Can't I have both bowtie and bowtie2 installed side by side?

[GenoMax]

Just saw this over at the TopHat site. Perhaps upgrading to latest Tophat may fix your problem.

Version 2.0.8 is a quick fix release addressing the following issues:

This version correctly handles the newest version of Bowtie2 v2.1.0.
The segment mapping slow-down introduced by some Bowtie2 parameter changes in version 2.0.7 is now corrected

There is also a new version of bowtie2 (v.2.1.0) available as well.

[rnavon]

Originally Posted by GenoMax

Just saw this over at the TopHat site. Perhaps upgrading to latest Tophat may fix your problem.

Thanks!
It wasn't on the site a couple of hours ago. I'll install the new tophat version and see if it helps.

[rnavon]

Updating Tophat from 2.0.7 to 2.0.8 solved the problem.