how to place bowtie in "PATH" for use with TopHat

[albrown415]

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.

[zorph]

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!

[albrown415]

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.

[albrown415]

Actually I was able to get it working using the description on the following webpage:

http://www.mac-forums.com/forums/os-x-darwin-development/201788-setting-my-environmental-path.html

Hope this helps anyone else with this problem.

[lmf_bill]

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.

[albrown415]

Thanks. I got it working earlier but my post didn't go through.

Thanks for your help.

[repinementer]

Having the slightly same problem

Although

I configured tophat in tophat folder it self

./configure --prefix=/home/bogugk/rnaseq/software/tophat-1.0.13

I set the path to Bowtie in tophat folder

export PATH=$PATH:/home/bogugk/rnaseq/software/bowtie-0.12.5

having error

[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?

[lmf_bill]

"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

[repinementer]

Ok. FInally I was able to install it by following your directions. thanx