Eliza, Perhaps you could consider looking into Amazon Web Services (AWS)? You'd then be able to test and access to a virtual machine with a supported OS for a few dollars, and then that would at least give you a working model system. In tpp/installer_linux you'll find scripts to completely configure the OS and download and install the TPP on AWS. Post here if you have any questions.
Hope this helps, Natalie On Sun, Sep 27, 2009 at 10:48 PM, Eliza <blond...@googlemail.com> wrote: > > Joe, > > I'd love to try it except I'm running x86 Debian Etch server. > > Eliza. > > On Sep 26, 1:20 am, Joe Slagel <jsla...@systemsbiology.org> wrote: >> Eliza, >> >> I may have another alternative for you, but I can't make any promises it'll >> work. I played around a little today with building rpb/deb packages for >> TPP. If your feeling experimental, your welcome to try downloading and >> installing it. You can get it from our ftp site >> atftp://ftp.systemsbiology.net/TPP/tpp_4.3.1-1_amd64.deb. This is a 64-bit >> AMD build, on Ubuntu 9.04 "server" that does not contain any dependencies >> (you'll still have to follow the TPP instructions to install them). If >> you have different platform/OS version I may be able to make another package >> that will work for you. >> >> To install it, use dpkg as so: >> >> % dpkg -i tpp_4.3.1-1_amd64.deb >> >> The default installation location is /usr/tpp. >> >> Cheers, >> Joe >> >> P.S. You should consider it very *EXPERIMENTAL* as I only tested a few >> simple operations. >> >> On Fri, Sep 25, 2009 at 2:00 PM, Joe Slagel >> <jsla...@systemsbiology.org>wrote: >> >> >> >> > Hi Eliza, >> >> > I was following this thread and all of the good advice you've been getting >> > to try to solve the problem. I think I saw in an email that you were using >> > Ubuntu 9.04. Is this correct, and do you know if its the desktop or server >> > and whether its 32 or 64 bit? >> >> > Thanks >> >> > On Thu, Sep 24, 2009 at 10:41 PM, Eliza <blond...@googlemail.com> wrote: >> >> >> Any more suggestions? There is quite a lot of interest in getting TPP >> >> running in the lab and at this point I am not sure how to proceed. >> >> >> On Sep 18, 8:15 pm, Brian Pratt <brian.pr...@insilicos.com> wrote: >> >> > (FWIW, Ubuntu is a flavor of Debian) >> >> >> > That's interesting - does "make clean all" work after your first "make >> >> > all"? It sounds like the build is somehow changing the environment, or >> >> > maybe even its own makefiles... >> >> >> > On Thu, Sep 17, 2009 at 11:45 PM, Eliza <blond...@googlemail.com> >> >> wrote: >> >> >> > > I haven't tried your suggestion of running it on another distro yet >> >> > > Natalie, but I did get the latest version when that was announced and >> >> > > I got a little bit further. I was able to run 'make all' without any >> >> > > errors, but when I run try to run 'make install' I'm back with the >> >> > > error message "Makefile.incl:431: /Makefile.pwiz.incl: No such file or >> >> > > directory >> >> > > make: *** No rule to make target `/Makefile.pwiz.incl'. Stop." >> >> >> > > I am not using Ubuntu, but Debian. >> >> >> > > On Sep 4, 8:40 pm, Natalie Tasman <natalie.tas...@insilicos.com> >> >> > > wrote: >> >> > > > Hi Eliza, >> >> >> > > > At this point, it might be worthwhile trying to compile the TPP on >> >> > > > another linux distribution that works well. For example, Ubuntu >> >> > > > 8.04. Then, I'd be sure to run the correct "install prerequisites" >> >> > > > file from tpp/installer_linux to make sure all the required system >> >> > > > packages are installed. >> >> >> > > > Then again, it wouldn't hurt to run the correct "install >> >> > > > prerequisites" for your own system. Currently, the Ubuntu 9.04 >> >> script >> >> > > > seems to work for 9.10 also, if you're using that. >> >> >> > > > Good luck, >> >> >> > > > Natalie >> >> >> > > > On Sep 4, 2009, at 1:05 AM, Eliza wrote: >> >> >> > > > > Mike - having an empty Makefile.config.incl didn't fix anything. >> >> I am >> >> > > > > still getting the error: make: *** No rule to make target `/ >> >> > > > > Makefile.pwiz.incl'. Stop. >> >> >> > > > > On Sep 1, 10:21 pm, Mike Coleman <tutu...@gmail.com> wrote: >> >> > > > >> Okay, this turned out to be useful. It appears that the contents >> >> of >> >> > > > >> your file 'Makefile.config.incl' is including itself (it appears >> >> to >> >> > > > >> be >> >> > > > >> a copy of 'Makefile.incl'). This recurses about 1000 times, at >> >> which >> >> > > > >> point you hit the file handle limit. The resulting error is >> >> > > > >> apparently ignored due to the '-include'. >> >> >> > > > >> So, either make 'Makefile.config.incl' an empty file, or >> >> otherwise I >> >> > > > >> think it should be just a short file including a few variable >> >> > > > >> definitions. Also, verify that neither of these files is a >> >> symbolic >> >> > > > >> or hard link to the other. >> >> >> > > > >> Probably this will fix things, or at least move things forward. >> >> >> > > > >> Mike >> >> >> > > > >> On Aug 31, 2:34 am, Eliza <blond...@googlemail.com> wrote: >> >> >> > > > >>> OK I have added make.strace.gz to the file uploads. >> >> >> > > > >>> On Aug 28, 6:34 pm, Mike Coleman <tutu...@gmail.com> wrote: >> >> >> > > > >>>> Okay, if you really want to bring out the big guns, do >> >> something >> >> > > > >>>> like >> >> > > > >>>> this >> >> >> > > > >>>> $ strace -f -s 1024 -v -o make.strace make >> >> >> > > > >>>> and put the resulting 'make.strace' log somewhere where we can >> >> > > > >>>> look at >> >> > > > >>>> it. I think this is erroring out pretty quickly, so hopefully >> >> that >> >> > > > >>>> log won't be too huge. No promises, but this may very well >> >> clarify >> >> > > > >>>> what's going wrong. >> >> >> > > > >>>> You'll have to install the strace package if it's not already >> >> > > > >>>> present. >> >> >> > > > >>>> Mike >> >> >> > > > >>>> On Aug 28, 4:59 am, Eliza <blond...@googlemail.com> wrote: >> >> >> > > > >>>>> That doesn't make any difference. >> >> >> > > > >>>>> On Aug 27, 8:12 pm, "Brian Pratt" <brian.pr...@insilicos.com> >> >> > > > >>>>> wrote: >> >> >> > > > >>>>>> Yeah, that's what we use here too. Perhaps you could try it >> >> as >> >> > > > >>>>>> a different, >> >> > > > >>>>>> newly created user? It sounds like there is something >> >> peculiar >> >> > > > >>>>>> about your >> >> > > > >>>>>> shell setup. >> >> >> > > > >>>>>> -----Original Message----- >> >> > > > >>>>>> From: spctools-discuss@googlegroups.com >> >> >> > > > >>>>>> [mailto:spctools-disc...@googlegroups.com] On Behalf Of >> >> Eliza >> >> > > > >>>>>> Sent: Thursday, August 27, 2009 12:13 AM >> >> > > > >>>>>> To: spctools-discuss >> >> > > > >>>>>> Subject: [spctools-discuss] Re: Failure with make >> >> >> > > > >>>>>> Bash >> >> >> > > > >>>>>> On Aug 20, 11:55 pm, "Brian Pratt" < >> >> brian.pr...@insilicos.com> >> >> > > > >>>>>> wrote: >> >> > > > >>>>>>> We basically tried that already: Eliza says the suggested >> >> >> > > > >>>>>>> export PWD=/opt/trans_proteomic_pipeline/src ; make all >> >> install >> >> >> > > > >>>>>>> did not work. She also tried the "SRC_ROOT= $(shell pwd)" >> >> > > > >>>>>>> change to the >> >> > > > >>>>>>> makefile. There's something deeper going on. >> >> >> > > > >>>>>>> Eliza, what shell do you use? I do see from googling that >> >> > > > >>>>>>> $PWD might be >> >> > > > >>>>>>> bash-specific, possibly there are other unintended bash >> >> > > > >>>>>>> dependencies. >> >> >> > > > >>>>>>> Brian >> >> >> > > > >>>>>>> -----Original Message----- >> >> > > > >>>>>>> From: spctools-discuss@googlegroups.com >> >> >> > > > >>>>>>> [mailto:spctools-disc...@googlegroups.com] On Behalf Of >> >> Mike >> >> > > > >>>>>>> Coleman >> >> > > > >>>>>>> Sent: Thursday, August 20, 2009 1:26 PM >> >> > > > >>>>>>> To: spctools-discuss >> >> > > > >>>>>>> Subject: [spctools-discuss] Re: Failure with make >> >> >> > > > >>>>>>> Eliza, >> >> >> > > > >>>>>>> I'mstill suspicious about the $PWD thing. If you're running >> >> > > > >>>>>>> 'make' >> >> > > > >>>>>>> normally, you might try something like >> >> >> > > > >>>>>>> $ PWD=$(pwd) make ... >> >> >> > > > >>>>>>> instead of just >> >> >> > > > >>>>>>> $ make ... >> >> >> > > > >>>>>>> to see whether that improves your situation. Alternatively, >> >> > > > >>>>>>> for the >> >> > > > >>>>>>> 'root' steps, you could do something like >> >> >> > > > >>>>>>> $ sudo PWD=$(pwd) make ... >> >> >> > > > >>>>>>> Mike >> >> > -- >> > Joe Slagel >> > Institute for Systems Biology >> > jsla...@systemsbiology.org >> > (206) 732-1362 >> >> -- >> Joe Slagel >> Institute for Systems Biology >> jsla...@systemsbiology.org >> (206) 732-1362 > > > > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
