I haven't built the TPP on OS X recently, but the build system
contains its own copy of the boost libraries. Can you tell if the TPP
build is using the TPP version of boost or the system library?
(I'd try to debug but my machines are on 10.7 and 10.8)
-Natalie
On Mon, Oct 1, 2012 at 4:24 PM,
are indeed
*consecutively* numbered (from 1 till 5'000 or more) in the raw data
when you browse them with the Agilent MassHunter Qual software. So my
guess is that there might still be something fishy about msconvert
here. My understanding was that the former converter (Trapper from
Natalie Tasman
Nice job on tracking that down. I'm sure there are other examples but
in TPP's src/mzXML/common directory you can look at the Base64 and
ScanConverter.cpp for code examples and some documentation on the
encoding.
-Natalie
On Fri, Feb 4, 2011 at 6:56 AM, dre shee...@gmail.com wrote:
Actually I
Have you done comparisons between mzXML output from your WINE
installation and a native Windows environment? I would expect that
there will be some subtle but important differences between the two.
Like I've said before on this list, and as Matt stated on this thread,
if you have this working
I wrote the pepXML viewer several years back. If you're comfortable
doing it, you could certainly write your own parsing code using XSLT
(blech) or use an xml parsing library in python, perl, etc. However,
I found that there was enough domain-specifc information and some
logic required to know
Hi Chanchal,
Take a look at the prerequisites which are listed for Centos. The TPP
is tested on fairly recent versions of Centos, which is very similar
similar to recent versions of RedHat Enterprise.
This file,
Bjorn,
As you already have macports installed, I suggest that you temporarily
move the sourceforge version of gnuplot out of the way, and then try
sudo port install gnuplot.
-Natalie
On Wed, Aug 25, 2010 at 12:22 PM, Bjorn caveman.bj...@gmail.com wrote:
I found that the png has something to
Hi Bjorn,
Looking at the error, I see that somehow it looks like you have a
comma-character in the filename
100805.LC2.IT2.XX.P01070_2-A,10_01_805.1940848714.gp
^
Please rename without this illegal character, try your analysis again,
and let us
Hi Bjorn,
If you can wait a bit for the upcoming TPP 4.4.0 release, I'll be glad
to lend my experiences. I routinely build on 10.6.4.
-Natalie
On Fri, Aug 13, 2010 at 5:33 AM, Bjorn caveman.bj...@gmail.com wrote:
Hi,
I'm trying to get TPP running on my computer (mac os 10.6.4) by
following
:
Meant, Natalie not Nicole. J apologies.
*From:* spctools-discuss@googlegroups.com [mailto:
spctools-disc...@googlegroups.com] *On Behalf Of *Natalie Tasman
*Sent:* Friday, July 16, 2010 5:52 PM
*To:* spctools-discuss@googlegroups.com
*Subject:* Re: [spctools-discuss] Error converting .d
Some simple advice: try the most recent version of msconvert from the
ProteoWizard project (an older version is included with the current TPP
release, but bugs may have been fixed since then).
MassHunter is no longer actively maintained and will likely be retired in
the upcoming TPP release.
The versions of perl you mention which the installer checks for were ones
available at the time of the last release, and we didn't want to use
versions which we didn't test against. The quickest fix for you would be to
just use perl 5.10, if that's possible. Otherwise, the installer logic for
It is possible to try the same analysis on the latest version of the
TPP and see if the problem has been already addressed? Please let us
know. If you still find the issue after testing the latest software,
please upload test files to the newsgroup's file section which
generate the same issue,
Yep-- use msconvert for anything mzML. It's included with the TPP,
and you will find a more recent version (recommended) from the
ProteoWizard website.
-Natalie
On Thu, Jun 24, 2010 at 10:12 AM, Jesse J firstblackphan...@gmail.com wrote:
Up till now I have just had ReAdW output mzXML, but when
Hi Nathan,
The search engines in pepXML are those which have been specifically
tested with the TPP. Regarding Matt's suggestion: as far as I
understand, the PSI groups are moving towards a new analysis standard:
http://psidev.info/index.php?q=node/319.
I haven't worked with that standard or
though they've had the code for about a year. I know
that Spectrum Mill and Phenyx have pepXML output as well.
Our group doesn't much care about validation errors due to an incomplete
schema enumeration, but having it in there would be nice.
-Matt
On 6/24/2010 1:19 PM, Natalie Tasman wrote
And if it's not working, just make sure that JAVA_HOME isn't defined
and the build will skip PepC.
-Natalie
On Mon, May 24, 2010 at 9:49 AM, Brian Pratt brian.pr...@insilicos.com wrote:
Hi Oded,
You'll need Java 1.6 - turns out javax.swing.table.TableRowSorter
isn't in 1.5. Can you readily
1) A guided tour of the Trans-Proteomic Pipeline
http://www3.interscience.wiley.com/journal/123261300/abstract?CRETRY=1SRETRY=0
2) http://tools.proteomecenter.org/wiki/index.php?title=TPP_Demo2009
-Natalie
On Mon, May 17, 2010 at 12:32 PM, Jesse J firstblackphan...@gmail.com wrote:
Um...that
I have not moved on to testing Ubuntu 10, but I have tested the latest
release on 8 and 9 (.04 and .10), and have scripts for installing all
required prerequisites on those systems (and some others) under svn trunk
tpp's installer_linux directory. Start by taking a look there.
Once you have the
Thank you, David. Ubuntu 10 users (or any other system), please feel free
to add notes or pages to the wiki. Email me if you need an account there.
:)
Natalie
On Fri, May 14, 2010 at 12:06 PM, David Trudgian
david.trudg...@path.ox.ac.uk wrote:
Hi Jesse,
This problem occurs because
When I hear audit I think of the mzML format instead of mzXML; you're
likely to find much more detailed metadata and clarification of
software-derived data in the newer format. mzML is also provided by
msconvert from ProteoWizard (and included with the TPP).
-Natalie
On 5/12/10 8:53 AM,
Hello,
I am forwarding this message to the ProteoWizard support list as well.
I don't know that anyhow has reliably gotten the converter software
to run under wine; at least for the the SPC converters (readw,
masswolf, trapper) wine is not a supported environment.
-Natalie
On Thu, May 6, 2010
Jacques,
I'm wondering if 64-bit perl installs to C:\Perl64 or something similar,
rather than the expeted C:\Perl. Can you please check?
Thanks,
Natalie
On 4/22/10 3:08 AM, Jacques wrote:
Hi everyone
I'm trying to install TPP (TPP_Setup_v4_3_JETSTREAM_rev_1.exe) on an
x64 Windows 2003 R3
The TPP's version of X!Tandem also uses expat, FYI.
-Natalie
On 4/1/10 2:14 AM, dctrud wrote:
Brian, Matt,
It now works nicely with all offset variables using boost::int64_t
(not unsigned as there is some setting to -1 in the code and within
expat the offsets are signed). Am able to work with
Hi Val,
This doesn't answer your questions, but right off the bat, I would
suggest dropping IE6 in favor of a modern, browser such as firefox,
chrome, or safari. IE6 is no longer popular due to security issues as
well as lack of standards, which the TPP is designed and tested
against. For
I see that in the current TPP (4.3.1) installer, we say TPP requires
ActivePerl version 5.8.8 or 5.10.x (available for free ActiveState, but
we are not allowed to distribute it directly). Please install ActivePerl
from [... ] and try the TPP installer again. However I see that the
links we
I am curious what version of the TPP you're trying to use. The current
windows installer should install and configure almost everything for you
(expect for ActivePerl, which you must install on your own; see the
related thread from today.) Why do you need VisualBasic? Also Java is
not
I haven't worked with that Perl module. But I would strongly suggest
that you first get the most current version of proteowizard's mscovert
working from the command-line, and then run this program as a shell
command from perl. msconvert, the recommended raw file converter, is
under rapid
To distribute your files, you could try posting them on the groups' file
page, and then reply with a post containing the filename:
http://groups.google.com/group/spctools-discuss/files
On 3/9/10 2:01 PM, Brian Pratt wrote:
I had a look at the three mzXML files you uploaded to Insilicos -
Hi Dave, Brian,
Just jumping into comment on Boost. Yes, it is welcomed and in fact
already used in the TPP (as well as the TPP-included ProteoWizard
project); however, because the Boost API and process of building Boost
libraries have not been particularly stable, we've found it necessary
Hello,
Have you tried the newer msconvert program, from the ProteoWizard
project? msconvert is included with the TPP; also, you may find a newer
version on the ProteoWizard website.
Please let us know how it goes.
-Natalie
On 2/1/10 4:05 PM, yinyin wrote:
Hello all,
In my case, ReAdw
Hi Angel,
I'm not familiar with Chef, but I am working on exactly this kind of
build process re-engineering. For various reasons (which I can detail
if interested,) I've decided to go with the tried and true autotools
system, and you can see the work that I'm doing in tpp's SVN under
Hi Bill,
For 4.3.x, I moved everything that was still needed from win_lib into
trunk/extern. I did this because people often didn't understand that
they had to download both directories (tpp and win_lib), and/or that
win_lib needed to match the exact version of tpp.
I maintained the Visual
Thank you, Angel.
By the way, I've also switched to MacPorts (vs Fink) for future TPP
development work, but haven't yet tested the TPP with 10.6 (I'm
waiting until 10.6.2 at least), so this is appreciated.
-Natalie
On Mon, Nov 2, 2009 at 12:32 PM, Angel delag...@gmail.com wrote:
I use
seem,
yet,
like a complicated enough problem to truly require one. And using
print statements is surely your quickest least intrusive route to
getting more information, since it can be done immediately, if you
can
already build successfully.
--Brendan
On Oct 6, 10:37 am, Natalie Tasman
Hi Bill,
While the currently support Visual Studio version for the TPP is the
(not-free) 2005 Professional version, you might want to first give the
(free) 2008 Express version a try. You would not be able to build the
SPC raw file converters (readw, etc), and you will probably turn up a
Just a reminder that trapper was developed and tested under 32-bit
Windows XP only. I have no idea if it works under Vista, or 64-bit.
You might want to look at the msconvert (included with the TPP) from
ProteoWizard; this program will replace trapper in the near future.
-Natalie
On Oct
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
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
.
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
Also, consider upgrading to TPP 4.3.1, which contains several bug fixes.
-Natalie
On Sep 22, 2009, at 8:32 AM, Brian Pratt wrote:
If it's really the same problem, then it's not a surprise that those
files don't exist, since the protXML file didn't get created,
because the pepXML file
In other words, you can access the TPP's web interface through your
usual web browser (like firefox, IE, chrome, safari, etc), but instead
of going to a website out on the internet, you're going to a
website that's running locally on your computer, through the
installed Apache webserver on your
Is it possible for you to completely uninstall your old version of
Apache, and then rerun the TPP installation? This should install, and
then properly configure Apache 2.2.
-Natalie
On Sep 15, 2009, at 11:32 AM, Michael wrote:
David,
I have a previous version of Apache installed
Sure, any 5.8.x series perl will work, and whatever the latest thing
that Active Perl recommends is fine.
-Natalie
On Sep 15, 2009, at 12:12 PM, AndrewK wrote:
I am about to load TPP on a new workstation. ActiveState shows
5.8.9.826 as the available binary download for x86 (winXP SP3).
version sensitive in
previous
releases, so it was a good question, and the right answer.
- Brian
On Tue, Sep 15, 2009 at 1:17 PM, Natalie Tasman
natalie.tas...@insilicos.com wrote:
Sure, any 5.8.x series perl will work, and whatever the latest thing
that Active Perl recommends is fine
Hello Andrew,
Please refer to my previous reply to your questions (topic: ReAdW DLL
installation location).
In short: ReAdW is not based on Extract_MSN. It is a different
program and has different requirements than Mascot Daemon (which comes
from Matrix Science, not the TPP). Rather,
I'm not a lawyer, but for what it's worth, a quick Google search
suggests that CDDL might be distributable with LGPL:
And by the way, the AAA string that you see is just the
encoding for an empty scan (as you've already seen, peaksCount will be
0 for these scans.)
On Sep 10, 2009, at 10:45 AM, Brian Pratt wrote:
I expect you'll find the difference between those computers is that
they have
We are proud to offer an update to the Trans-Proteomic Pipeline (TPP)
software, release 4.3.1 (4.3 revision 1). The software is available for
Windows as well as linux (and unofficially) through osx source from all the
usual locations (please see the section below, Getting the software).
Most
Hello Oded,
Please see the recently released 4.3.1 version of the TPP, which
contains the fix that you mention.
Best wishes,
Natalie
On Sep 9, 2009, at 12:49 PM, Oded wrote:
Hi ,
Is it possible to get this bug fix (thanks again Brian) into windows
installation package?
Thanks,
Oded
Hi Mike,
Thanks for your efforts with helping Eliza, and for your good thoughts
and comments. I'd like to respond to a few things:
1) Boost in the TPP: I'd like to clarify how we've set things up. The
included Boost under tpp/extern is compiled and used without any
system interactions
Hello Dominik, Jimmy,
Besides my recommendation to try msconvert, which is the program with
more developer focus at this point, there is already a command-line
option in the 4.3 series ReAdW program. I'd added this feature
because Thermo's software did not understand which scan to report
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
Hi Andrew,
Currently, 32-bit XP with current service packs is the supported and
tested Windows OS for the TPP, although if you search this newsgroup
you'll find people's experiences with 64-bit and Vista. My impression
is that things don't necessary work out of the box for the TPP, due to
: /Makefile.pwiz.incl: No such file or directory
make: *** No rule to make target `/Makefile.pwiz.incl'. Stop.
On Aug 5, 10:25 pm, Natalie Tasman natalie.tas...@insilicos.com
wrote:
Hi Eliza,
It sounds like something strange is going on. Maybe you should re-
load the sourcecode. Also, I've
Hello Bright,
That link is correct. SourceForce (the hosting site) may have been
temporarily inacessible, but I just tried it and it works.
For Windows, you want to find TPP v4.3 (jetstream) rev 0 and
download the setup exe file.
Natalie
On Tue, Aug 11, 2009 at 9:23 AM,
Trans-Proteomic Pipeline (TPP) 4.3.0 release notes
We are proud to offer a major update to the Trans-Proteomic Pipeline
(TPP) software, release 4.3.0 (4.3 revision 0). The software is
available for Windows as well as linux (and unofficially) through osx
source from all the usual locations
Thanks, Mike. And yes, this is the preferred place for technical
discussions (patches, bug reports) as well.
Natalie
On Aug 6, 2009, at 8:52 AM, tutu...@gmail.com wrote:
$ gzip --test XML_sample_files.tgz
gzip: XML_sample_files.tgz: invalid compressed data--format
violated
My
Hi Eliza,
I haven't run into this before, but you may want to try a make
distclean; make sequence. I would also look at the compiler output
earlier in the stream and see if there were any uncaught errors
building the AminoAcid that might provide a clue.
Please let us know how it goes,
Hi Scott,
Thanks for your feedback and I'm glad David is taking a look. I just
want to remind everyone that svn trunk (which you're working with) is
development code. If you want stable results stick with the official
releases.
-Natalie
On Tue, Jul 28, 2009 at 6:35 PM, Scott
directly to .pep.xml files using mspire. Its not much of a
pipeline anymore but it does the job.
Regards
Ali
On Jul 15, 9:19 pm, Natalie Tasman natalie.tas...@insilicos.com
wrote:
Hi Ali,
Greg made some good comments on your post regarding the Sequest search
engine. I'm curious
Hi David,
This is an operating system issue, not due to the trapper program
itself, and the answer will be the same for any command-line program.
Simply surround the entire filename with quotes, and that should do
the trick.
(Consider that without quotes, the program has no way to know for sure
files using mspire. Its not much of a
pipeline anymore but it does the job.
Regards
Ali
On Jul 15, 9:19 pm, Natalie Tasman natalie.tas...@insilicos.com
wrote:
Hi Ali,
Greg made some good comments on your post regarding the Sequest search
engine. I'm curious as to what search engine
Natalie Tasman wrote:
Hi Chris,
Just a reminder that the masswolf centroid mode is experimental, as
noted in the usage statement.
Matt, how is PWIZ centroiding? Can msconvert be used to apply this
signal processing and output a processed mzXML file?
-Natalie
On Wed, Jul 15
Hi Chris,
Just a reminder that the masswolf centroid mode is experimental, as noted in
the usage statement.
Matt, how is PWIZ centroiding? Can msconvert be used to apply this signal
processing and output a processed mzXML file?
-Natalie
On Wed, Jul 15, 2009 at 11:57 AM, Chris Hughes
, but
doesn't generate the mzXML file. I suppose what I want to know is
this: When the GUI version runs the command 'ReAdW etc' where does it
read the ReAdW file from? In another words, How can I know the path
from which the GUI runs ReAdW?
Thanks
Ali
On Jul 7, 6:02 pm, Natalie Tasman natalie.tas
Hi Jake,
Sorry to hear that you ran into a glitch. We're making some changes
to the way we integrate ProteoWizard (pwiz) and the TPP. You might
want to either revert to a slightly earlier (unstable dev) trunk
revision, or switch to the (stable) production 4.2.1 branch.
Best,
Natalie
Hi Jake,
It sounds like an issue with the boost libraries. In trunk, I've
moved those into the actual trunk branch and they should be
automatically built for you. However in 4.2.1, you need to also have
the corresponding win_lib directory checked out (for example, if you
have tpp from
Hello Ali,
It sounds like you're using the command-line version of the converter
(ReAdW). The easiest way to get started with the TPP on Windows is
to download the complete TPP installer, which will set up and
configure a web-based interface. This interface should be a lot
easier to use.
If you
Hi MIchelle,
This program was not tested under Vista, and I'm not sure if it
works. I recommend XP or 2003 if you have access. But some quick
checks: do you have Waters MassLynx installed on the same machine, and
can you open the file in question under MassLynx? Also, I'm not sure
if
Hello Antonio,
The mzXML files should correspond to the same raw file input used for
your Sequest search. For example if starting from a Thermo .raw file,
you'd convert that mzXML, search that, and then convert the search
results to pepXML.
Note that the pepXML files refer to specific
in the process of
development?
Bernard
On Jun 25, 5:46 am, Natalie Tasman natalie.tas...@insilicos.com
wrote:
Hello,
First, you might want to check that the file extention is
indeed .raw
and not .RAW. Capitalization might make a difference.
Can you open this file in the Waters
error msg in command prompt and Windows pops up a
masswolf.exe has encountered a problem and needs to close error
report. Is the centroiding function still in the process of
development?
Bernard
On Jun 25, 5:46 am, Natalie Tasman natalie.tas...@insilicos.com
wrote:
Hello,
First, you
is comitted so that I can continue with some small
tests ;-)
Cheers
Andreas
On Jun 24, 2009, at 9:49 PM, Natalie Tasman natalie.tas...@insilicos.com
wrote:
Hello Andreas,
I have fixed the problem in trunk's Makefile.incl. Please note that
we're still waiting for another fix to get
Hello Gautam,
The version of X!Tandem which is bundled with both Windows and linux
versions of the TPP includes the k-score plugin. We routinely use
this algorithm on both systems.
-Natalie
On May 5, 2009, at 9:07 AM, Taejoon Kwon wrote:
Hi Gautam,
I am running X!Tandem with k-score
to: E08_101023_SchizoS1.mzXML.new
-
I guess this is not so important since this does not disturb the
subsequent workflow, but I just wanted to mention this to you.
Thanks again,
Best,
Ludovic
On Apr 1, 10:08 pm, Natalie Tasman ntas...@systemsbiology.org wrote:
Hello Ludovic
Hi Ilya,
Did you try using the parameter switch I suggested for specifying the level?
-Natalie
On Mon, May 4, 2009 at 2:09 AM, Ilya.Agron ilya.ag...@gmail.com wrote:
to Natalie:
I've downloaded the latest version of TPP and reinstalled it.
Strange, it doesn't process anything. When I
Eli,
PS-- probably you have seen that the same options you have in
MassHunter for deisotoping are available for the trapper converter
when run from the command-line?
-Natalie
On Mon, May 4, 2009 at 2:09 AM, Ilya.Agron ilya.ag...@gmail.com wrote:
to Natalie:
I've downloaded the latest
Hi Illya,
MsXML2Search is the current version of the TPP tool that does this
(MsXML2Other is retired).
It's included with the TPP, and you can see all of the options by
running this program without any arguments. To specify MS level
besides the default of 2, use the -M option.
Please
Hi there Jamie,
Just to be clear, the two programs that you mentioned aren't from the
Seattle Proteome Center (SPC), and you might find more support if you write
directly to those programs' maintainers. But if anyone else on the list has
experience, of course they are welcome to respond here.
Hello Federico,
It's definitely not a stupid question. As you know, Scaffold is a
commercial product. They claim a reimplementation of some of the TPP's core
algorithms from the original publications. In the years since those
publications, there have been continual improvements and refinements
which seems to be incorrect.
What do you think?
Thanks,
Federico
On Apr 17, 7:25 pm, Natalie Tasman ntas...@systemsbiology.org wrote:
Hi Federico,
I've changed the title of this thread to reflect the issue at hand. Can you
see the spectra through alternate means? For example, for the same
Hi Federico,
I've changed the title of this thread to reflect the issue at hand. Can you
see the spectra through alternate means? For example, for the same file,
use the PepXMLViewer to find the ID with the same scan number and click on
the ions link.
-Natalie
On Fri, Apr 17, 2009 at 8:35 AM,
to
start.
-Natalie
On Fri, Apr 17, 2009 at 3:10 AM, brennmat brenn...@gmail.com wrote:
On Apr 16, 6:29 pm, Natalie Tasman ntas...@systemsbiology.org wrote:
Hi Mattias,
To get started with Xcalibur, you might want to look at the XDK for
examples.
That's what I did. I looked at the HTML
Hi Mattias,
To get started with Xcalibur, you might want to look at the XDK for
examples.
But I do think it will be easier if you can just use and/or adapt existing
tools. I know that Matt from the ProteoWizard (PWIZ) project (including in
the TPP) has been interested in parsing chromatogram
Hi Oded,
You are correct; this was a feature with a very old version of the pepXML
display that isn't currently active. The current viewer is strictly
read-only, so far. This hasn't been a very high priority so far as
xinteract and the prophets do the most common filtering (probabilities), but
Hi Kristian,
Also, 4.2.1 contained many bug fixes. I'm not sure if this would have been
addressed, but it's always most efficient for us if you can try to replicate
the issue on the latest version.
-Natalie
On Thu, Apr 16, 2009 at 12:42 PM, Christine Vogel vogel@gmail.comwrote:
I have
...@gmail.com
wrote:
Hi Natalie,
I would like to note that (4) is *necessary* for building TPP with MSVS
2005 SP1 *if* MSVS 2008 has been installed under the same Windows.
Regards
Dmitrii
Natalie Tasman wrote:
Hi Dmitri,
I may have misunderstood you in 2) above: you do want
I doubt that you are actually trying to access the old Agilent2mzXML code
(which is no longer supported here, actually-- Trapper is the current
Agilent .d MassHunter converter.) That xml_out might be specific to the
old Agilent2mzXML project.
You will be better served searching the SVN
Hi Dmitri,
Thanks for sharing your notes. Hopefully you found some of the text in the
README_WIN.txt file at the top level helpful as well.
Reponding to your points:
2) qualscore is not used by the TPP build process, but is required by the
TPP installer build process. Win_lib *is* extensively
as well.
-Natalie
On Mon, Apr 13, 2009 at 2:17 PM, Carl Manaster carl.manas...@gmail.comwrote:
Hi, Natalie,
Again, thanks for the prompt response.
On Apr 13, 1:31 pm, Natalie Tasman ntas...@systemsbiology.org wrote:
I doubt that you are actually trying to access the old Agilent2mzXML code
Hi Bill,
Regarding your first message:
Sounds like your running into incompatibilities with your boost version and
the expected version. In this older version of the TPP, you'll want to look
in the Makefile and possibly edit that file to match the installed versions
on your machines; Boost
Hi Carl,
One last suggestion: MzXML2Search -dta will produce a directory of dta files
corresponding to your mzXML file. And also, look at MzXML2Search, which has
some filter options of it's own.
Here's an idea that's less efficient with CPU and disk, but I wonder if you
could save some effort
Hi Dmitri,
I may have misunderstood you in 2) above: you do want to download qualscore,
trans_proteomic_pipeline, and win_lib (either from trunk or whatever branch
you're working in)-- the other directories are not needed, as you suggested.
-Natalie
On Mon, Apr 13, 2009 at 1:40 PM, Natalie
Look in tpp/src/release (or debug, depending on your build configuration.)
-Natalie
On Fri, Apr 10, 2009 at 9:03 AM, Carl Manaster carl.manas...@gmail.comwrote:
Hi, Natalie,
All of this said, assuming that you have VS2005 Professional:
1) check out trunk/tpp
2) check out trunk/win_lib
PS-- you can find this by looking at the project properties. If there's a
macro like (SOLUTION_DIR) you can edit the field and click a little macro
button to see what those expand too-- at least on VS 2005 Pro.
Best,
N
On Fri, Apr 10, 2009 at 10:41 AM, Natalie Tasman ntas...@systemsbiology.org
if you'd like me to build a binary for you for
windows or linux.
Best,
Natalie
On Wed, Apr 8, 2009 at 10:12 AM, Natalie Tasman
ntas...@systemsbiology.orgwrote:
Hello Ben,
Last year I spent quite a lot of time working with Agilent to exactly
replicate the behavior of their MassHunter mzData
Thanks, Matt. That's great to learn that you've found the MFC dependency to
be unnecessary!
-Natalie
On Thu, Apr 9, 2009 at 2:17 PM, Matthew Chambers
matthew.chamb...@vanderbilt.edu wrote:
Hi Carl,
MFC is not actually a requirement for using XRawfile, only COM. As far
as I can tell,
Hi Carl,
I'm glad to hear it. Again, you're on your own with anything except VS 2005
Professional (at least for official support.)
It's quite helpful to hear your experiences, and please feel free to
contribute any useful code and/or build changes that you come up with.
-Natalie
On Thu, Apr
Hello Ben,
Last year I spent quite a lot of time working with Agilent to exactly
replicate the behavior of their MassHunter mzData exporter, including
thresholding. I'm sorry that this isn't working for you. These
threshold flags should work. As you know from beta-testing the
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