problems with tophat failing to find bowtie (MacOSX)

[martinobarenco]

Dear Forum,

I have tried to install tophat on a new mac machine, and although both bowtie and tophat seem to be installed just fine, it seems tophat has trouble finding bowtie. Here is what I get when I run the test command for tophat:

pc248-23:test_data martinobarenco$ tophat -r 20 test_ref reads_1.fq reads_2.fq

[Wed Sep 22 16:04:37 2010] Beginning TopHat run (v1.0.11)
-----------------------------------------------
[Wed Sep 22 16:04:37 2010] Preparing output location ./tophat_out/
[Wed Sep 22 16:04:37 2010] Checking for Bowtie index files
[Wed Sep 22 16:04:37 2010] Checking for reference FASTA file
[Wed Sep 22 16:04:37 2010] Checking for Bowtie
[FAILED]
Error: bowtie not found on this system

bowtie is installed on the system and the path has been set in .bash_profile:

pc248-23:test_data martinobarenco$ bowtie --version
bowtie version 0.12.7
64-bit
Built on Franklin.local
Tue Sep 7 14:27:57 PDT 2010
Compiler: gcc version 4.0.1 (Apple Inc. build 5493)
Options: -O3 -m64
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}

I have tried to change the versions of tophat (tophat-1.0.14.OSX_x86_64 and tophat-1.0.13, the latter installed "by hand" and with appropriate changes in the PATH in either case) and I get the same results. It worked fine on a linux machine (with v1.0.11) so it must be problem to OSX (and most likely something I did wrong there). Anyone met the same issue?

Many thanks,

Martino

[Jon_Keats]

Hi,

I recently got it running on a new Mac with OSX10.6.4 using bowtie version bowtie-0.12.6-macos-10.5-x86_64 and tophat version 1.0.14.OSX_x86_64. Looks like you are using an old version of tophat with the newest version of bowtie so maybe there is a compatibility issue?

[martinobarenco]

Thanks for the reply. I did try the latest versions of tophat (1.0.14) and bowtie (12.7), both the 64 bits precompiled versions, to no avail. I even tried to change the version of python, again with no success. I'll write directly to the maintainers and report back here if a solution can be found.

[martinobarenco]

I have narrowed the problem down to some glitch in python, so it is certainly not an issue of compatibility problems between tophat and bowtie.

I have looked at the tophat script and noticed that the exception is thrown when the "Popen" command in the "subprocess" library is called (line 600 or so in the script). However, calling bowtie works fine when using a different library (os). Also subprocess works fine on python itself. (the commands are shown below).

I also get the exact same results when reverting to the original apple python that shipped with the computer rather than the Enthought Python Distribution.

Jon, where did you specify your PATH for locating tophat/bowtie (mine are in .bash_profile)? many thanks.

M.

pc248-23:~ martinobarenco$ python
Enthought Python Distribution -- http://www.enthought.com
Version: 6.2-2 (32-bit)

Python 2.6.5 |EPD 6.2-2 (32-bit)| (r265:79063, May 28 2010, 15:13:03)
[GCC 4.0.1 (Apple Inc. build 5488)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import subprocess
>>> proc = subprocess.Popen(['bowtie', '--version'],stdout=subprocess.PIPE)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/Library/Frameworks/Python.framework/Versions/6.2/lib/python2.6/subprocess.py", line 633, in __init__
errread, errwrite)
File "/Library/Frameworks/Python.framework/Versions/6.2/lib/python2.6/subprocess.py", line 1139, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
>>> import os
>>> os.system('bowtie --version')
bowtie version 0.12.7
64-bit
Built on Franklin.local
Tue Sep 7 14:27:57 PDT 2010
Compiler: gcc version 4.0.1 (Apple Inc. build 5493)
Options: -O3 -m64
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}
>>> proc = subprocess.Popen(['python', '--version'],stdout=subprocess.PIPE)
>>> Python 2.6.5 -- EPD 6.2-2 (32-bit)


0

[martinobarenco]

*edited repeat posting*

[martinobarenco]

sorted

One needs to put the absolute paths in the .bash_profile files ie, in my case:

/Users/martinobarenco/Documents/NGS/tools/bowtie/bowtie-0.12.7:

*not*:

~/Documents/NGS/tools/bowtie/bowtie-0.12.7:

and it works. Although I don't quite understand why the paths relative to the home directory work under linux (with .bashrc) and why the "os" library in python recognises these relative paths but not the "subprocess" library. Oh well...