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Old 06-08-2010, 12:38 PM   #1
albrown415
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Default how to place bowtie in "PATH" for use with TopHat

Hello,
I'm trying to get TopHat running but am getting the following error about not being able to find bowtie:

>>python tophat -r 20 test_ref reads_1.fq reads_2.fq

[Fri Jun 4 12:53:41 2010] Beginning TopHat run (v1.0.11)
-----------------------------------------------
[Fri Jun 4 12:53:41 2010] Preparing output location ./tophat_out/
[Fri Jun 4 12:53:41 2010] Checking for Bowtie index files
[Fri Jun 4 12:53:41 2010] Checking for reference FASTA file
[Fri Jun 4 12:53:41 2010] Checking for Bowtie
[FAILED]
Error: bowtie not found on this system



I am working on a Mac OS X machine and am unsure how to specify a "path". I usually place the program in the working directory. In this case, I have a TopHat directory where I've placed everything (the test data, the reference set, the TopHat executables, and the bowtie executables):

bed_to_juncs juncs_db test_ref.2.ebwt
bowtie library_stats test_ref.fa
bowtie-build long_spanning_reads test_ref.rev.1.ebwt
bowtie-inspect mask_sam test_ref.rev.2.ebwt
closure_juncs prep_reads tophat
contig_to_chr_coords reads_1.fq tophat_out
extract_reads reads_2.fq tophat_reports
fix_map_ordering segment_juncs
gff_juncs test_ref.1.ebwt


Any suggestions for how to get the computer to find Bowtie?
Thanks.
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Old 06-08-2010, 12:45 PM   #2
zorph
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Depending on the shell you're using, you'll be doing the following:

• If you are using the Bash shell, you have to edit the ".bashrc" file in your home directory by adding the following two (2) lines of code at the end:

o PATH=$PATH:/path/to/bowtie/0.12.5
o export PATH

• If you are using the C shell, you have to edit the ".cshrc" file in your home directory by adding the following one (1) line to the end:

o set path = (/path/to/bowtie/bowtie/0.12.5 $path)

Hope this helps. To make sure it's in your path, you should just be able to type in "Bowtie" and the program should be brought up. Good Luck!

Last edited by zorph; 06-08-2010 at 12:52 PM.
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Old 06-08-2010, 01:36 PM   #3
albrown415
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Thanks for the quick reply, however, I'm still not sure how to change the path.

How do I locate the bashrc on my computer? Does Mac OS X have this file? I'm having trouble locating it.

To run TopHat, I'm currently typing the TopHat command directly into the Mac OS X Terminal.

I believe that the Terminal program is based on bash. (When I typed "env | grep", I got "SHELL=/bin/bash"). Is this the Bash shell you're talking about? Will I be able to change the path by changing a setting in the Terminal?

Alternatively, I feel like it should be easier to simply place bowtie in the TopHat directory. I've tried this and it's not working, but am hoping that it's simply a matter of determining the right combination of files in the working directory.

Thanks.
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Old 06-08-2010, 01:53 PM   #4
albrown415
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Actually I was able to get it working using the description on the following webpage:

http://www.mac-forums.com/forums/os-...ntal-path.html

Hope this helps anyone else with this problem.
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Old 06-08-2010, 02:11 PM   #5
lmf_bill
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just do as zorph said. I think you need learn something about Linux/Unix/Mac.
.bashrc or .bash_profile locate in your home folder.
In the terminal, you can use "cd ~" to enter. then use "ls -a" you can see ".bashrc" or ".bash_profile" file; use vi .bashrc (or .bash_profile) to edit it; use "source .bashrc" (or .bash_profile)to enable it,

good luck! if still not work, you really need more reading.
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Old 06-08-2010, 03:00 PM   #6
albrown415
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Thanks. I got it working earlier but my post didn't go through.

Thanks for your help.
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Old 06-14-2010, 05:21 AM   #7
repinementer
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Default Having the slightly same problem

Although

I configured tophat in tophat folder it self

Quote:
./configure --prefix=/home/bogugk/rnaseq/software/tophat-1.0.13
I set the path to Bowtie in tophat folder

Quote:
export PATH=$PATH:/home/bogugk/rnaseq/software/bowtie-0.12.5
having error
Code:
[bogugk@Trivia bin]$ ./tophat -r 20 /home/bogugk/rnaseq/software/test_data/test_ref.fa /home/bogugk/rnaseq/software/test_data/reads_1.fq /home/bogugk/rnaseq/software/test_data/reads_2.fq 

[Mon Jun 14 20:19:26 2010] Beginning TopHat run (v1.0.13)
-----------------------------------------------
[Mon Jun 14 20:19:26 2010] Preparing output location ./tophat_out/
[Mon Jun 14 20:19:26 2010] Checking for Bowtie index files
Error: Could not find Bowtie index files /home/bogugk/rnaseq/software/test_data/test_ref.fa.*
Traceback (most recent call last):
  File "./tophat", line 1635, in ?
    sys.exit(main())
  File "./tophat", line 1556, in main
    (ref_fasta, ref_seq_dict) = check_index(bwt_idx_prefix)
  File "./tophat", line 634, in check_index
    check_bowtie_index(idx_prefix)
  File "./tophat", line 569, in check_bowtie_index
    exit(1)
TypeError: 'str' object is not callable
But I didn't give any path to BOWtie? is it causing the problem?

Last edited by repinementer; 06-14-2010 at 05:25 AM.
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Old 06-14-2010, 06:12 AM   #8
lmf_bill
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"export PATH only change the current session. Once you log out, anything you've added to the path will be removed. "

If you do not log out, I guess tophat does not accept this way of PATH setting. (I do not try this way)

The way to modify the path variable permanently is to edit .bash_profile (assuming you are using the default bash shell).

Maybe, it will help you
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Old 06-14-2010, 08:29 PM   #9
repinementer
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Ok. FInally I was able to install it by following your directions. thanx

Last edited by repinementer; 06-14-2010 at 10:41 PM.
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