Hi Ross, I'm not an install guru. I've only done it on Ubuntu linux. Check your Makefile_config.incl file for "errors" in your path specifications? Maybe that is where the path problem originated. If so a rebuild is in order. If not then some one else might know if its an apache config issue.
Also note that the paths are hard coded in the tandem search result files and some others that are generated, like the tandem.params files, the pep.xml files. You can look at the tandem search result file in a terminal and see what the path specification is there also. Good luck, 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 2:15 PM, Ross <[email protected]> wrote: > 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<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]> 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<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<http://localhost/tpp/data/demo/tandem/tandem-style.xsl> >>> >>> Can anyone help? >>> Thanks >>> >>> -- >>> You received this message because you are subscribed to the Google >>> Groups "spctools-discuss" group. >>> To unsubscribe from this group and stop receiving emails from it, send >>> an email to spctools-discu...@**googlegroups.com. >>> To post to this group, send email to spctools...@googlegroups.**com. >>> Visit this group at http://groups.google.com/** >>> group/spctools-discuss?hl=en<http://groups.google.com/group/spctools-discuss?hl=en> >>> . >>> For more options, visit >>> https://groups.google.com/**groups/opt_out<https://groups.google.com/groups/opt_out> >>> . >>> >>> >>> >> >> -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/spctools-discuss?hl=en. > For more options, visit https://groups.google.com/groups/opt_out. > > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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