Hi Joe,
I went down numerous envar PATHs with no success.
However, I think it turned out to be my mistake when editing the first
install tpp_gui_config.pl file I put the paths in the wrong place:
THIS DOESN'T WORK:
#
# SET ENVIRONMENT VARIABLES HERE
'base_dir' => '/usr/local/tpp/',
'www_root' => '/usr/local/tpp/',
'data_dir' => '/usr/local/tpp/data/',
'ttpbin' => '/usr/local/tpp/bin/',
#
# you can uncomment the next lines to tell TPP to gzip pepXML and
protXML for more efficient storage and file transfer
# (also see the doMzXMLGzip setting below)
$ENV{'PEPXML_EXT'} = ".pep.xml.gz";
$ENV{'PROTXML_EXT'} = ".prot.xml.gz";
my %settings = ( # don't change this line, either!
#
# SET TPP_GUI DEFAULTS HERE
# See tpp_gui.pl readconfig() calls for a list
# of what can be set here.
#
After a re-install to the /usr/local/apps/tpp path I edited the
tpp_gui_config.pl file to be the below and now all works fine:
THIS DOES WORK:
#
# SET ENVIRONMENT VARIABLES HERE
#
# you can uncomment the next lines to tell TPP to gzip pepXML and
protXML for more efficient storage and file transfer
# (also see the doMzXMLGzip setting below)
$ENV{'PEPXML_EXT'} = ".pep.xml.gz";
$ENV{'PROTXML_EXT'} = ".prot.xml.gz";
my %settings = ( # don't change this line, either!
#
# SET TPP_GUI DEFAULTS HERE
# See tpp_gui.pl readconfig() calls for a list
# of what can be set here.
#
'base_dir' => '/usr/local/apps/tpp/',
'www_root' => '/usr/local/apps/tpp/',
'data_dir' => '/usr/local/apps/tpp/data/',
'tppbin' => '/usr/local/apps/tpp/bin/',
# for example, you might want to uncomment the next line to make x!
tandem your default search engine.
I added "export PATH=$PATH:/usr/local" to /etc/apache2/envvar
previously and that didn't solve the problem. Probably should make
that more restrictive now or just remove it to see if it still works
or if it breaks it.
So I think it was just that Petunia didn't know where to look because
I put the directives in the wrong section of the tpp_gui_config.pl??
Thanks Joe for your help!
Brian
On Feb 29, 2:19 pm, Joseph Slagel <[email protected]>
wrote:
> 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
>
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