Okay, thanks for you help Brian. I'll carry on posting here in the hope that someone can help.
Here is a paste of my Makefile.config.incl: TPP_ROOT=/usr/local/tpp/ TPP_WEB=/tpp/ ## for Boost BOOST_INCL=-I/usr/include/boost/ BOOST_LIBDIR=/usr/lib BOOST_LIBSPEC=-gcc43-mt LINK=shared LIBEXT=so PERL_LIB_CORE=/usr/lib64/perl5/CORE TPP is installed in /usr/local/tpp. Has anyone else had experience of this problem? On Thursday, April 4, 2013 7:39:34 PM UTC+1, Brian Hampton wrote: > > 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] <javascript:>>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] <javascript:>. >> To post to this group, send email to >> [email protected]<javascript:> >> . >> 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. 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.
