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
>>
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