I got Petunia to work after reading <https://groups.google.com/group/
spctools-discuss/browse_thread/thread/8137caeb56f39945#>
Based on the SPCTools Wiki for installing tpp in Ubuntu 10.04.3 called
for installing in /usr/local/tpp. I have seen many posts where tpp is
installed in /usr/local/apps/tpp. I didn't know if that path might be
hard coded somewhere so I recompiled for the install to the later path
e.g. /usr/local/apps/tpp as the install dir. I also changed the
following in tpp/cgi-bin/tpp_gui.pl to read:
my $data_dir = readconfig('data_dir',"${www_root}data/");
# full path to data directory top-level
The original code inserted ISB/ in front of data/.
The tpp_gui_config.pl additions for my setup are:
# SET TPP_GUI DEFAULTS HERE
# See tpp_gui.pl readconfig() calls for a list
# of what can be set here.
#
'base_dir' => '/usr/local/apps/tpp/',
'www_root' => '/usr/local/apps/tpp/',
'data_dir' => '/usr/local/apps/tpp/data/',
'tppbin' => '/usr/local/apps/tpp/bin/',
#
Now *almost* everything works. I can't view the results
of .interact.pep.shtml or .interact.protein.shtml.
Brian
On Feb 29, 10:55 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
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