Ron, Here's a compiled Mascot2XML.exe binary for you:
http://tinyurl.com/24a8jna Regarding the errors you're seeing yourself, I'd just type 'make' in the 'src' directory in your msys/mingw window. I don't know how to target building just a specific binary but hopefully another developer can chime in with instructions if possible. - Jimmy On Fri, Jul 2, 2010 at 10:13 AM, Ronald W. Finnegan <r...@mail.nih.gov> wrote: > I downloaded the MascotConverter.cxx rev 4945 checked in by Jimmy on > 4-15-10 and copied it to this location within the TPP source > distribution: C:\TPP431src\tpp\src\Parsers\Algorithm2XML\Mascot2XML\ > > I am getting these errors when I run the makefile command: > > lnt...@nimh-lntvm1 /c/tpp431src/tpp/src > $ makefile mascot2xml > ./makefile: line 52: /c/tpp431src/tpp/src/: is a directory > ./makefile: line 53: include: command not found > ./makefile: line 56: FASTAR_DIR: command not found > ./makefile: line 57: syntax error near unexpected token `${LGPL},1' > ./makefile: line 57: `ifeq (${LGPL},1) ' > > can someone please provide a suggestion as to how i might get this to > work? > > thanks > > Ron > > On Jul 1, 8:36 pm, Brian Pratt <brian.pr...@insilicos.com> wrote: >> Have a look at >> this:http://tools.proteomecenter.org/wiki/index.php?title=TPP:Building_Win... >> >> On Thu, Jul 1, 2010 at 3:00 PM, Ronald W. Finnegan <r...@mail.nih.gov> wrote: >> >> >> >> > can you recommend a compiler that i can use to run makefile on a 64 >> > bit windows server? >> >> > On Jul 1, 1:42 pm, Brian Pratt <brian.pr...@insilicos.com> wrote: >> >> You'll need to get the entire source tree from >> >> /sashimi/trunk/trans_proteomic_pipeline/ down, them cd to >> >> /sashimi/trunk/trans_proteomic_pipeline/src and "make _Mascot2XML". >> >> >> On Thu, Jul 1, 2010 at 9:58 AM, Ronald W. Finnegan <r...@mail.nih.gov> >> >> wrote: >> >> >> > I have downloaded the MascotConverter.cxx source file. >> >> >> > How do I compile the MascotConverter file so that the TPP source file >> >> > dependencies are met? >> >> >> > On Jul 1, 12:35 pm, Jimmy Eng <jke...@gmail.com> wrote: >> >> > >http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/trans_proteom... >> >> >> > > This just points you to the Mascot2XML source files (which are >> >> > > dependent on other source files in the TPP project). >> >> >> > > On Thu, Jul 1, 2010 at 6:22 AM, Ronald W. Finnegan >> >> > > <r...@mail.nih.gov> wrote: >> >> >> > > > Jimmy, >> >> >> > > > I am using the Mascot2XML from the last TPP version released >> >> > > > 9-9-2009. Can you please point me to the trunk where I can download >> >> > > > rev 4945 from your April 15, 2010 check-in? >> >> >> > > > thanks >> >> >> > > > Ron >> >> >> > > > On Jun 30, 7:02 pm, Jimmy Eng <jke...@gmail.com> wrote: >> >> > > >> I have faint memories of dealing with this but I'm away from work >> >> > > >> so >> >> > > >> can't confirm. This might've been fixed in rev 4945 check-in on >> >> > > >> April >> >> > > >> 15th; my check-in log message for Mascot2XML was "parsing update >> >> > > >> for >> >> > > >> entry with protein n-term modification which doesn't seem to be >> >> > > >> handled by current code". >> >> >> > > >> Are you able to compile Mascot2XML from trunk and see if the >> >> > > >> problem >> >> > > >> goes away? Otherwise, I'll follow-up with this next week when I'm >> >> > > >> back at work. >> >> >> > > >> On Tue, Jun 29, 2010 at 5:59 AM, Ronald W. Finnegan >> >> > > >> <r...@mail.nih.gov> wrote: >> >> >> > > >> > Can anyone tell me if this bug reported back in April 2009 has >> >> > > >> > been >> >> > > >> > fixed: >> >> >> > > >> > Thermo Orbitrap RAW file is inputted into tpp -> convert to >> >> > > >> > mzxml -> >> >> > > >> > convert to mgf -> run mascot -> convert to pepXML >> >> >> > > >> > The problem is as follows: >> >> >> > > >> > When I use the mascot default modification Acetyl (protein >> >> > > >> > N-term), >> >> > > >> > the TPP converter that converts the mascot output .DAT file to >> >> > > >> > pepXML >> >> > > >> > format creates the following header in the pepXML file: >> >> >> > > >> > <aminoacid_modification aminoacid=" " mass="42.010559" >> >> > > >> > massdiff="42.010559" peptide_terminus="n" variable="Y"/> >> >> > > >> > <aminoacid_modification aminoacid="N" mass="156.053486" >> >> > > >> > massdiff="42.010559" peptide_terminus="n" variable="Y"/> >> >> > > >> > <aminoacid_modification aminoacid="-" mass="42.010559" >> >> > > >> > massdiff="42.010559" peptide_terminus="n" variable="Y"/> >> >> > > >> > <aminoacid_modification aminoacid="t" mass="42.010559" >> >> > > >> > massdiff="42.010559" peptide_terminus="n" variable="Y"/> >> >> > > >> > <aminoacid_modification aminoacid="e" mass="42.010559" >> >> > > >> > massdiff="42.010559" peptide_terminus="n" variable="Y"/> >> >> > > >> > <aminoacid_modification aminoacid="r" mass="42.010559" >> >> > > >> > massdiff="42.010559" peptide_terminus="n" variable="Y"/> >> >> > > >> > <aminoacid_modification aminoacid="m" mass="42.010559" >> >> > > >> > massdiff="42.010559" peptide_terminus="n" variable="Y"/> >> >> >> > > >> > If you look at this header closely, the entries are not only >> >> > > >> > meaningless, but there is something funny to be seen if you look >> >> > > >> > at >> >> > > >> > the aminoacid="" entries: >> >> >> > > >> > aminoacid=" " >> >> > > >> > aminoacid="N" >> >> > > >> > aminoacid="-" >> >> > > >> > aminoacid="t" = N - term >> >> > > >> > aminoacid="e" >> >> > > >> > aminoacid="r" >> >> > > >> > aminoacid="m" >> >> >> > > >> > as far as I know the aminoacid property should indicate aminoacid >> >> > > >> > letters and not be spelling out N-term. This is obviously a >> >> > > >> > parsing >> >> > > >> > error occurring somewhere during the conversion. >> >> >> > > >> > Here is the link the original thread: >> >> >> > > >> >http://groups.google.com/group/spctools-discuss/browse_thread/thread/... >> >> >> > > >> > thanks >> >> >> > > >> > Ron >> >> >> > > >> > -- >> >> > > >> > You received this message because you are subscribed to the >> >> > > >> > Google Groups "spctools-discuss" group. >> >> > > >> > To post to this group, send email to >> >> > > >> > spctools-disc...@googlegroups.com. >> >> > > >> > To unsubscribe from this group, send email to >> >> > > >> > spctools-discuss+unsubscr...@googlegroups.com. >> >> > > >> > For more options, visit this group >> >> > > >> > athttp://groups.google.com/group/spctools-discuss?hl=en.-Hidequotedtext >> >> > > >> > - >> >> >> > > >> - Show quoted text - >> >> >> > > > -- >> >> > > > You received this message because you are subscribed to the Google >> >> > > > Groups "spctools-discuss" group. >> >> > > > To post to this group, send email to >> >> > > > spctools-disc...@googlegroups.com. >> >> > > > To unsubscribe from this group, send email to >> >> > > > spctools-discuss+unsubscr...@googlegroups.com. >> >> > > > For more options, visit this group >> >> > > > athttp://groups.google.com/group/spctools-discuss?hl=en.-Hidequoted >> >> > > > text - >> >> >> > > - Show quoted text - >> >> >> > -- >> >> > You received this message because you are subscribed to the Google >> >> > Groups "spctools-discuss" group. >> >> > To post to this group, send email to spctools-disc...@googlegroups.com. >> >> > To unsubscribe from this group, send email to >> >> > spctools-discuss+unsubscr...@googlegroups.com. >> >> > For more options, visit this group >> >> > athttp://groups.google.com/group/spctools-discuss?hl=en.-Hide quoted >> >> > text - >> >> >> - Show quoted text - >> >> > -- >> > You received this message because you are subscribed to the Google Groups >> > "spctools-discuss" group. >> > To post to this group, send email to spctools-disc...@googlegroups.com. >> > To unsubscribe from this group, send email to >> > spctools-discuss+unsubscr...@googlegroups.com. >> > For more options, visit this group >> > athttp://groups.google.com/group/spctools-discuss?hl=en.- Hide quoted text >> > - >> >> - Show quoted text - > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to spctools-disc...@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. > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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