Brian, I think your PATH environment variable isn't including the TPP bin directory. You could try adding it to envvars like so and restarting Apache:
echo "PATH=$PATH:/usr/local/tpp/bin:" | tee -a /etc/apache2/envvars If this solves you problem please let me know and I'll update the instructions. (And feel free to look over what the actual paths are in your PATH and remove any that might not be appropriate for a web server). -joe On Wed, Feb 29, 2012 at 7:55 AM, Brian Hampton <[email protected]> wrote: > Hello, > > I have installed TPP 4.5.2 on Ubuntu 10.10 using the instructions here > <http://tools.proteomecenter.org/wiki/index.php? > title=TPP_4.5.2:_Installing_on_Ubuntu_10.04.3> > > In those instructions there are a couple of errors where chown is used > when the command should be chmod. However, I believe I have the > correct ownership and permissions on the directories and files for > execution by apache2 but when I try to do any analysis via the web > interface it fails. See below: > > As root I can successfully execute the below command from a shell but > if I su to www-data which is the user apache2 runs as I get $ sh: > Tandem2XML: not found Even if I execute it in the /usr/local/tpp/bin > directory. > > Help please. > > Thanks in advance, > > Brian Hampton > > > > This is the command being submitted through the tpp_gui.pl: > > cd /usr/local/tpp/ISB/data; Tandem2XML /usr/local/tpp/ISB/data/ > 120223_S1782-SDS_eHILLIC-frac-1.tandem /usr/local/tpp/ISB/data/ > 120223_S1782-SDS_eHILLIC-frac-1.tandem > > Here is the result: > > # Commands for session T8PMKUQEN on Wed Feb 29 10:26:24 2012 > # BEGIN COMMAND BLOCK > ###### BEGIN Command Execution ###### > [Wed Feb 29 10:26:24 2012] EXECUTING: cd /usr/local/tpp/ISB/data; > Tandem2XML /usr/local/tpp/ISB/data/120223_S1782-SDS_eHILLIC- > frac-1.tandem /usr/local/tpp/ISB/data/120223_S1782-SDS_eHILLIC- > frac-1.tandem > OUTPUT: > sh: Tandem2XML: not found > END OUTPUT > RETURN CODE:32512 > ###### End Command Execution ###### > # All finished at Wed Feb 29 10:26:24 2012 > # END COMMAND BLOCK > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
