Tophat can't find Bowtie

[biznatch]

I've just downloaded Tophat and am trying to use it for the first time by testing it as described in the Tophat "Getting Started" section with the provided test data and I get the error "Error locating program: bowtie". I have my bowtie (and tophat and samtools) folder added to PATH and am not sure why I'm getting this error. I'm not sure if it's necessary but I also gave the bowtie executable all permissions (chmod 777) and that doesn't help.

Also, when I type bowtie or tophat from any directory they run (since they're in PATH) but if I type sudo bowtie or sudo tophat I get the error "command not found". Just out of curiosity, why would this be? I'm not too familiar with permissions, etc. in Linux (I'm using Ubuntu). I added the relevant folders to PATH by adding the following to the end of .bashrc:

export PATH="$PATH:~/chip/bowtie/"
export PATH="$PATH:~/chip/tophat/"
export PATH="$PATH:~/chip/samtools/"

[Bukowski]

Sudo does not inherit $PATH from the user on Ubuntu. You can alleviate this by putting something like this in your ~/.profile or ~/.bashrc:

alias sudo='sudo env PATH=$PATH'

As for the rest of your issue, perhaps setting the full path to the folder rather than using the tilde shortcut and see if it helps (although I'm not sure why it would).

You can save lines in your .bashrc with:

export PATH="$PATH:~/chip/bowtie:~/chip/tophat:~/chip/samtools"

No need to chain multiple export commands

[biznatch]

I combined the multiple export PATH lines into one and replaced the ~ with the full path for each but I'm still having the same problem. In the terminal I get:

[Wed Nov 9 12:28:01 2011] Beginning TopHat run (v1.3.3)
-----------------------------------------------
[Wed Nov 9 12:28:01 2011] Preparing output location ./tophat_out/
[Wed Nov 9 12:28:01 2011] Checking for Bowtie index files
[Wed Nov 9 12:28:01 2011] Checking for reference FASTA file
[Wed Nov 9 12:28:01 2011] Checking for Bowtie
Error locating program: bowtie

I know that bowtie is correctly added to PATH because I can run Bowtie itself fine, it's just a problem with Tophat finding it... :S

Edit: I tried some stuff and now it finds Bowtie...but not Samtools...the adventure continues...

[jazstappung]

Could you explain how to fix the PATH of bowtie?
Because i have this problem whit the Testing the installation in the "getting started" manual.

[ystappung@bio-fcr test_data]$ /home/ystappung/sources/tophat-1.4.0.Linux_x86_64/tophat -r 20 test_ref reads_1.fq reads_2.fq

[Wed Jan 18 16:20:27 2012] Beginning TopHat run (v1.4.0)
-----------------------------------------------
[Wed Jan 18 16:20:27 2012] Preparing output location ./tophat_out/
[Wed Jan 18 16:20:27 2012] Checking for Bowtie index files
[Wed Jan 18 16:20:27 2012] Checking for reference FASTA file
[Wed Jan 18 16:20:27 2012] Checking for Bowtie
Error locating program: bowtie



thanks