Hi James, Do you know what xsl processor you are using on your system? It may well be that our generated xsl is incompatible with it (we use xsltproc). Can you try using a different one and see what happens? Cheers, --Luis
On Mon, Jun 25, 2012 at 8:17 AM, sirlark <[email protected]> wrote: > Hi Brian, > > Thanks for the swift reply. I remember seeing the SSI thread before. I tried > it, and Interprophet suddenly started seg faulting. Turns out it was > something else i did around the same time, but I never got around to > re-enabling the SSI includes. I have done so now, and I can view .shtml > links, but I'm still getting the runtime errors when running InterProphet, > and I still only see 1 truncated protein's output. > > Thanks, > James > > > On Monday, 25 June 2012 16:12:33 UTC+2, Brian Hampton wrote: >> >> Hello James, >> >> When this happened to me it turned out to be an Apache problem. My >> install of Apache2 didn't have SSI includes enabled. Luis pointed me in the >> right direction to find that out... Below is my reply to the list when I >> got it working. I hope yours is as easy to fix. >> >> Cheers, >> >> Brian >> >> >> Hi Luis, >> Thanks so much for your help. Indeed the Apache2 default install >> conveniently does not have SSI includes enabled. A simple a2enmod include >> and a restart of apache did the trick. >> >> Thanks for the tip. I can now use the complete TPP on a data set and >> actually see the results! >> >> Thanks, >> >> Brian Hampton >> >> >> >> On Monday, June 25, 2012 8:46:20 AM UTC-4, sirlark wrote: >>> >>> Hi, >>> >>> Firstly, I'm using TPP v4.5 RAPTURE rev 2, Build 201202071404 (linux) >>> >>> I've tried running protein prophet three different ways, with different >>> results. >>> >>> The first way, I analyse peptides without choosing to run interprophet. >>> Then I run proteinprophet on the interact.pep.xml file. It runs fine, no >>> complaints. But when I try to view the file, I get this error: >>> >>> Error loading stylesheet: Parsing an XSLT stylesheet failed. >>> >>> The second way, I analyze peptides without choosing to run interprophet. >>> Then I run interprophet on the single interact.pep.xml file, and then >>> proteinprophet on the interact.iproph.pep.xml, marking "input is from >>> Iprophet". Again, viewing the results I get >>> >>> Error loading stylesheet: Parsing an XSLT stylesheet failed. >>> >>> The third way is the same as the second way excpet I also check >>> "pregenerate html file" (in the hopes of bypassing the XSLT error. During >>> the run I see the following output, and >>> >>> [Mon Jun 25 14:06:19 2012] EXECUTING: /usr/local/tpp/bin/protxml2html.pl >>> -file /usr/local/tpp/data/ValidationSet/0000/interact.prot.xml HTML >>> OUTPUT: >>> Writing results to html file: >>> /usr/local/tpp/data/ValidationSet/0000/interact.prot.html >>> runtime error: file >>> /usr/local/tpp/data/ValidationSet/0000/interact.prot.xsl line 197 element >>> param >>> Unexpected XSLT element 'param'. >>> runtime error: file >>> /usr/local/tpp/data/ValidationSet/0000/interact.prot.xsl line 197 element A >>> Variable 'mypep' has not been declared. >>> xmlXPathCompiledEval: evaluation failed >>> Done! >>> END OUTPUT >>> >>> View interact.pep.xml gives the same XSLT error, and viewing the >>> interact.pep.html shows truncated output for a single protein. >>> >>> If I log in to the TPP server and view the interact.pep.xml files using >>> less/cat, all the info seems to be there. >>> >>> Thanks, >>> James > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To view this discussion on the web visit > https://groups.google.com/d/msg/spctools-discuss/-/2keL64Ect8sJ. > > 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=en. -- 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=en.
