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
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