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.
