The work Insilicos did to make TPP compatible with Amazon EC2 was done completely on Ubuntu 8, and that was all fine with Petunia. But its true that when I've moved other projects from Ubuntu 8 to 9 and 10 I did find the that wheels came off in new and interesting ways each time. I should probably take a poke at building an Ubuntu 10.4-based TPP machine image.
What kind of problems were you finding? It's worth noting that there are probably some unintended assumptions in the Petunia viewers about the data being processed via Petunia as well. Brian On Sat, May 15, 2010 at 6:15 AM, EricTan <[email protected]> wrote: > It's good to know there is a fair number of people using TPP under > Ubuntu. I've installed TPP 4.3.1 in Ubuntu 10.04 and 9.10 just about > two weeks back. I tested the applications by going through the TPP > Demo2009 tutorial (http://tools.proteomecenter.org/wiki/index.php? > title=TPP_Demo2009). The files I edited to make TPP work are: > > 1) extern/xtandem/src/Makefile > => Change GCC to 4_3, i.e. from "CXXFLAGS = -O2 -DGCC4 - > DPLUGGABLE_SCORING $(OSFLAGS) $(ZLIB_INCL) -DREAD_GZIP -I ../../ > gzstream $(PWIZ_MZML_FLAGS)" to "CXXFLAGS = -O2 -DGCC4_3 - > DPLUGGABLE_SCORING $(OSFLAGS) $(ZLIB_INCL) -DREAD_GZIP -I ../../ > gzstream $(PWIZ_MZML_FLAGS)". > > 2) extern/xtandem/src/saxhandler.h > => Add "#include <stdint.h>", as mentioned by David. > > 3) extern/xtandem/src/stdafx.h > => Change the includes within "#ifdef GCC4_3" && "#endif" to > reflect: "#include <stdio.h>", "#include <stdlib.h>" and "#include > <string.h>". > => Ref: bill's reply on > http://groups.google.com.sg/group/spctools-discuss/browse_thread/thread/ef67c1f2dfd696/. > > Reading this thread, it appears that adding "#include <stdint.h>" to > extern/xtandem/src/saxhandler.h is all that is needed to get TPP > working in Ubuntu. So I'm just sharing what I've done in case it helps > someone else. > > To all the Ubuntu users out there, do you run TPP applications via > commandline or via the Petunia web-interface? I can't quite get > applications running from Petunia; I suspect it's my user / user group > + permissions settings. After acquiring the result files of the TPP > Demo2009 tutorial by running the applications commandline, I tried > viewing the files using Petunia and had mixed successes. So I am > wondering if anyone had gotten TPP running fully via Petunia on > Ubuntu. I would certainly appreciate if you could shed some light on > this. > > Cheers > Eric > > -- > 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. > > -- 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.
