Hi Austin, While I can't say for certain what the problem is I would suspect that it could either be that your PATH did not contain /usr/local/apps/tpp/bin when you launched Apache or the tpp_gui.pl program has the incorrect hard coded path to the program. You can check the latter by running:
% grep out2xml /usr/local/apps/tpp/cgi-bin/tpp_gui.pl If the results are not a absolute path then its probably the former issue. I would stop apache, set your PATH variable, and then restart apache. -Joe On Tue, Nov 17, 2009 at 5:24 PM, Austin <[email protected]> wrote: > Hi Everyone, > > I started setting up the TPP on Ubuntu 9.04 / Apache2 over the weekend > following the instructions found at > > http://tools.proteomecenter.org/wiki/index.php?title=TPP_4.2.1:_Installing_on_Ubuntu_9.04 > , > and have had a few minor issues (so far). The setup seems to have gone > fine, and I can log into /tpp/cgi-bin/tpp_gui.pl and all that jazz. > > The first issue I encountered in creating PepXML files from .out > files. When I attempt to do the processing through the GUI, all of the > files fail with the error: > > sh: Out2XML: not found > END OUTPUT > RETURN CODE:32512 > > and no .pep.xml files are produced. However, if I run the same command > in a terminal: > > $> cd /usr/local/apps/ISB/data/Tutorial; Out2XML /usr/local/apps/ISB/ > data/Tutorial/raft4041 1 -P/usr/local/apps/ISB/data/Tutorial/ > sequest.params -Etrypsin > > there are no issues. I've added /usr/local/apps/tpp/bin to my $PATH > variable, and this seems to work for everything except the TPP GUI. > Any ideas? > > The second issue I've encountered is when trying to view the .pep.xml > files through the PepXML viewer. At the top of the page I get the > error: > > Messages > Unable to access xml file via webserver, so cannot check xml file > for changes () > Check webserver configuration if desired. > (URL: undefined) > > The peptides get loaded, so it seems that the xml parsing goes as > planned. However, the page is unable to load the stylesheet and the > "PeptideAtlas" images. If I try to get to that image directly (http:// > localhost/tpp/html/images/pa_tiny.png) I receive a 500 internal server > error. Any ideas where the problem may lie? I've sifted through the > virtual host configuration a bit and haven't found any obviously > offending lines. I can use PeptideProphet and ProteinProphet from the > command line, but without the front end the utility is greatly > diminished. Any help is greatly appreciated! > > - Austin > > -- > > 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]<spctools-discuss%[email protected]> > . > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=. > > > -- Joe Slagel Institute for Systems Biology [email protected] (206) 732-1362 -- 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=.
