Hi Brian,
Thanks for your reply.
I followed the tutorial to install the TPP, please find a paste of my
tpp_config_gui.pl just in case.
Further information: this does not happen when opening the pep.xml files
that were converted from these tandem files, in the same tutorial step. It
is the tandem files that I cannot view.
Do you have any other ideas?
Thanks
============================
#
# this is where you can add customization of the tpp_gui.pl script without
it being
# destroyed by a software update.
#
sub readconfig { # don't change this
my($key, $default) = @_; # don't change this
# do not change anything above this line, it will break everything.
#
# 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/tpp/',
'www_root' => '/usr/local/tpp/',
'data_dir' => '/usr/local/tpp/data/',
'tppbin' => '/usr/local/tpp/bin/',
# for example, you might want to uncomment the next line to make x!tandem
your default search engine.
# 'pipeline' => 'Tandem', # one of [Sequest Mascot SpectraST Tandem]
# or you might uncomment this so all your raw files convert to .mzXML.gz to
save space.
# 'doMzXMLGzip' => true,
# or you might want to uncomment the next line to change your mascot server
setup.
# 'mascot_server' => "http://myotherserver/mascot/";,
'dummy' => 0); # don't change this
return $settings{$key} || $default; # don't change this
} # don't change this
1; # required so that file can be correctly included in another script
#- gives a 'true' response when loaded
==========================================
On Thursday, April 4, 2013 5:43:49 PM UTC+1, Brian Hampton wrote:
>
> Hi Ross,
>
> Check your tpp_config_gui.pl file for correct paths. See this page for
> e.g. a linux install:
>
>
> http://tools.proteomecenter.org/wiki/index.php?title=TPP_4.5.2:_Installing_on_Ubuntu_10.04.3
>
> Brian Hampton
> Protein Analysis Lab
> Center for Vascular and Inflammatory Diseases
> University of Maryland School of Medicine
> 800 West Baltimore Street Rm 307
> Baltimore MD 21201
> V: 410-706-8207
> F: 410-706-8234
>
>
> On Thu, Apr 4, 2013 at 10:59 AM, Ross <[email protected] <javascript:>>wrote:
>
>> Hi all
>> I've got TPP 4.6.2 installed on a Fedora 17 64-bit box. I'm just going
>> through the tutorial (demo2009).
>>
>> After searching the mzML files using X!Tandem, clicking on the output
>> files takes me to a page with a 'not found' error, with this URL:
>>
>> http://localhost/data/demo/tandem/OR20080317_S_SILAC-LH_1-1_01.tandem
>>
>> The data isn't stored here; the path is missing a tpp/ entry, I think it
>> should look like this:
>>
>> http://localhost/*tpp/*
>> data/demo/tandem/OR20080317_S_SILAC-LH_1-1_01.tandem
>>
>> I'm unsure where the config is to change this...?
>>
>> Also, when I manually change the URL to include /tpp, the page reports:
>>
>> Error loading stylesheet: A network error occurred loading an XSLT
>> stylesheet:http://localhost/tpp/data/demo/tandem/tandem-style.xsl
>>
>> Can anyone help?
>> Thanks
>>
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