New TPP Release: Version 3.2.0 SQUALL

[Joshua Tasman]

Dear SPC Tools Users,

We are releasing the next revision of the Trans-Proteomic Pipeline,
version 3.2.0 - SQUALL (cygwin package ISB-MS-Tools-3.2-0a; please note,
the cygwin distribution name now follows the current TPP version). This
update includes the following changes and improvements:

Cygwin Developer Tools:

o Based on feeback, the dev tools are now an *optional* part of the
installation. To include these, go to the "proteomics" section in the
installer and choose the "ISB-MS-Tools-dev" package.

PeptideProphet:

o Beta Phenyx support
- support of .pepXML Phenyx output extension
- users must specify xinteract options via commandline:
-D<database path>
-a<datapath>

o XTandem tuning of Discriminant Function Mixture Modeling

o More intuitive reimplementation of Gamma Distribution

o Auto skipping over files that have PeptideProphet results or aren't
pepXML

Performance optimizations for Q3ProteinRatioParser and
XpressProteinRatioParser from LabKey:

o 257x speed up on a 1.8MB Xpress protXML file, 1025x speedup on a 13MB
Q3 protXML file, 3495x speedup (or more) on a 75MB Q3 protXML file
(completed in 2 minutes 53 seconds, formerly gave up on it after a full
week of processing.)

o Improvement to XML parsing

o And various other bug fixes.

For downloading and installing the Windows version please visit the
following guide on our wiki:
"http://tools.proteomecenter.org/wiki/index.php?title=TPP:User_Documentation"

For downloading the sourcecode please go to the following link:
"http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=126912"

Everyone is encouraged to read and contribute to our wiki, at
http://tools.proteomecenter.org/wiki/

Thanks for your continued use, support, and feedback!

The SPC Tools team: Luis, David, Josh

[jtasman]

Dear SPC Tools Users,

The cygwin distribution has been updated with a very small bug fix. The new cygwin package is ISB-MS-Tools-3.2-0b and will be reinstalled simply by rerunning the TPP_Cygwin_setup.exe installer program.

For those interested, the system would become confused if input and output filenames were similar.

Linux users, please update
/trans_proteomic_pipeline/src/Visualization/InteractParser/InteractParser.cxx
from CVS source.

The SPC Tools team: Luis, David, Josh

[Joshua Tasman]

Dear SPC Tools Users,

We are releasing the next revision of the Trans-Proteomic Pipeline,

version 3.2.1 - SQUALL (cygwin package ISB-MS-Tools-3.2-1b). This

update includes the following changes and improvements:

o) X!Tandem with K-Score plugin is now included as a cygwin binary.
While we are still refining the PeptideProphet modeling of tandem
results, this should allow early adopters to play via the command-line,
and brings us close to providing a completely open-source, free,
proteomics solution! Source can be included by selecting the source
package under "Proteomics".

o) Pep3D
1) improves to interface: links are only generated if showing one
mzXML file (otherwise there is serious potential of returning an
enormous html file when multiple mzXML files in same analysis, esp.
from high-res intruments)

2) Minor changes to input form elements: Changed text for 'resolution'
and 'size' for clarity

o) Important fix to ASAPRatio results browser (fixing occasional
crashes/missing data display)

o) Fix to xinteract, which would have become confused if input and
output names were similar

and various other bug fixes.

=> For downloading and installing the Windows version please visit the

following guide on our wiki:
"http://tools.proteomecenter.org/wiki/index.php?title=TPP:User_Documentation"

=> For downloading the sourcecode please go to the following link:
"http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=126912"

=> Everyone is encouraged to read and contribute to our wiki, at
http://tools.proteomecenter.org/wiki/

[Joshua Tasman]

Dear SPC Tools Users,

We are releasing the next revision of the Trans-Proteomic Pipeline,

version 3.2.2 - SQUALL (cygwin package ISB-MS-Tools-3.2-2d). This
update includes many changes and improvements and all users are
recommended to update their software.

NOTE: Cygwin users, please download and save the TPP_Cygwin_Setup.exe
program. Usually this does not need to be re-downloaded when the TPP is
updated, but the setup program itself has been updated to version 2.578.
http://tools.proteomecenter.org/software/TPP_Cygwin_Setup.exe

Some of the changes in the TPP 3.2.2 release include:

o) X!Tandem (with K-Score plugin): Cygwin distribution now contained
standard-named "tandem.exe". Linux source tree includes tandem source.

o) Tandem2XML: fixes for n-terminal modifications, and modifications
with greater than 3 digits left of the decimal point.

o) new program: Sqt2XML: converts SQT files into pepxml suitable for
searching with the TPP. Contributed by our new TPP developer Matt
Chambers-- thanks, Matt!

and many other bug fixes.

=> For downloading and installing the Windows version please visit the

following guide on our wiki:
"http://tools.proteomecenter.org/wiki/index.php?title=TPP:User_Documentation"

=> For downloading the sourcecode please go to the following link:
"http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=126912"

=> Everyone is encouraged to read and contribute to our wiki, at
http://tools.proteomecenter.org/wiki/

The SPC Tools team: Josh, David, Luis

[Joshua Tasman]

The TPP has been updated to correct the missing ProteinProphet protein
annotation issue (cygwin package ISB-MS-Tools-3.2-2e). Linux users may
update source from

http://sashimi.svn.sourceforge.net/svnroot/sashimi/branches/release_3-2-2

Josh

[Greg Bowersock]

I just tried a fresh install this afternoon and found a couple of issues:

 

For Linux users that are using out2summary, you will need to modify:

misc/out2summary/out2summary.c

Uncomment the Unix definition for Sep and comment out the Windows definition.
As someone must have made this minor change recently.

 

Also, before you run make configure, you should change the following file:

CGI/show_help.pl:

Change: $CGI_HOME = '/tpp/cgi-bin/';    to $CGI_HOME = '/tools/bin/TPP/tpp/cgi-bin/';

 

You can change the above file after installation, but substitute the full path to your cgi-bin directory in the replacement line, otherwise the Help page won't work.

 

Greg
 

[Alex]

Hi all,

I'm trying to compile the latest version updated, but I'm encountering
some problems. Cannot complete the "make all". I SVNed the TPP using
the branches/release_3-2-2/trans_proteomic_pipeline. Just modifed the
out2summary as Greg stated and tried to compile. It looks like the
Makefile doesn't try to see which system it is (32 versus 64) and
looks for the libs in /usr/lib/* instead of looking in in /usr/lib64/*
as we are working on a 64 machine. I just tried to change the makefile
as follows and it goes a little bit further but not complete:

#
# cygwin or linux?
#
ifeq (${OS},Windows_NT)
OSFLAGS= -D__CYGWIN__
GD_LIB= /lib/libgd.a
BOOST_REGEX_LIB= /lib/libboost_regex-gcc-mt.a
else
OSFLAGS= -D__LINUX__
GD_LIB= -lgd
# BOOST_REGEX_LIB= /usr/lib/libboost_regex.a -lpthread
BOOST_REGEX_LIB= -lboost_regex -lpthread
endif

I just uploaded two "compile_log.txt" files in the file section that
contains the error messages before and after changes to the Makefile.

Thanks for any help.

Alex

On Sep 20, 10:40 pm, "Greg Bowersock" <bowers...@gmail.com> wrote:
> I just tried a fresh install this afternoon and found a couple of issues:
>
> For Linux users that are using out2summary, you will need to modify:
> misc/out2summary/out2summary.c
> Uncomment the Unix definition for Sep and comment out the Windows
> definition.
> As someone must have made this minor change recently.
>
> Also, before you run make configure, you should change the following file:
> CGI/show_help.pl:
> Change: $CGI_HOME = '/tpp/cgi-bin/'; to $CGI_HOME =
> '/tools/bin/TPP/tpp/cgi-bin/';
>
> You can change the above file after installation, but substitute the full
> path to your cgi-bin directory in the replacement line, otherwise the Help
> page won't work.
>
> Greg
>

> On 9/19/07, Joshua Tasman <jtas...@systemsbiology.org> wrote:
>
>
>
>
>
> > The TPP has been updated to correct the missing ProteinProphet protein
> > annotation issue (cygwin package ISB-MS-Tools-3.2-2e). Linux users may
> > update source from
>

> >http://sashimi.svn.sourceforge.net/svnroot/sashimi/branches/release_3...

>
> > Josh
>
> > Joshua Tasman wrote:
>
> > > Dear SPC Tools Users,
>
> > > We are releasing the next revision of the Trans-Proteomic Pipeline,
> > > version 3.2.2 - SQUALL (cygwin package ISB-MS-Tools-3.2-2d). This
> > > update includes many changes and improvements and all users are
> > > recommended to update their software.
>
> > > NOTE: Cygwin users, please download and save the TPP_Cygwin_Setup.exe
> > > program. Usually this does not need to be re-downloaded when the TPP is
> > > updated, but the setup program itself has been updated to version 2.578.
> > >http://tools.proteomecenter.org/software/TPP_Cygwin_Setup.exe
>
> > > Some of the changes in the TPP 3.2.2 release include:
>
> > > o) X!Tandem (with K-Score plugin): Cygwin distribution now contained
> > > standard-named "tandem.exe". Linux source tree includes tandem source.
>
> > > o) Tandem2XML: fixes for n-terminal modifications, and modifications
> > > with greater than 3 digits left of the decimal point.
>
> > > o) new program: Sqt2XML: converts SQT files into pepxml suitable for
> > > searching with the TPP. Contributed by our new TPP developer Matt
> > > Chambers-- thanks, Matt!
>
> > > and many other bug fixes.
>
> > > => For downloading and installing the Windows version please visit the
> > > following guide on our wiki:
> > > "

> >http://tools.proteomecenter.org/wiki/index.php?title=TPP:User_Documen...

> > "
>
> > > => For downloading the sourcecode please go to the following link:
> > > "

> >http://sourceforge.net/project/showfiles.php?group_id=69281&package_i...

> > "
>
> > > => Everyone is encouraged to read and contribute to our wiki, at
> > > http://tools.proteomecenter.org/wiki/
>

> > > The SPC Tools team: Josh, David, Luis- Hide quoted text -
>
> - Show quoted text -

[Greg Bowersock]

Have you tried to make the changes that were mentioned in this thread:

http://groups.google.com/group/spctools-discuss/browse_thread/thread/538267de15d0974f

 

The issues in that thread are most likely what is causing the problem.

 

Greg

 

> > annotation issue (cygwin package ISB-MS-Tools-3.2-2e ).  Linux users may

[Joshua Tasman]

Hi Alex,

Greg is correct. You'll also need to change
src/Visualization/PepXMLViewer/Makefile as well. Please let us know if
that works.

Josh

Greg Bowersock wrote:
> Have you tried to make the changes that were mentioned in this thread:
> http://groups.google.com/group/spctools-discuss/browse_thread/thread/538267de15d0974f
>
> The issues in that thread are most likely what is causing the problem.
>
> Greg
>
>

> On 9/21/07, *Alex* <alexandre...@gmail.com

> <mailto:bowers...@gmail.com>> wrote:
> > I just tried a fresh install this afternoon and found a couple of
> issues:
> >
> > For Linux users that are using out2summary, you will need to modify:
> > misc/out2summary/out2summary.c
> > Uncomment the Unix definition for Sep and comment out the Windows
> > definition.
> > As someone must have made this minor change recently.
> >
> > Also, before you run make configure, you should change the
> following file:
> > CGI/show_help.pl:
> > Change: $CGI_HOME = '/tpp/cgi-bin/'; to $CGI_HOME =
> > '/tools/bin/TPP/tpp/cgi-bin/';
> >
> > You can change the above file after installation, but substitute
> the full
> > path to your cgi-bin directory in the replacement line, otherwise
> the Help
> > page won't work.
> >
> > Greg
> >
> > On 9/19/07, Joshua Tasman < jtas...@systemsbiology.org

> <http://sourceforge.net/project/showfiles.php?group_id=69281&package_i.>..

[Alex]

Exactly the right problem. Thanks.
I had already fixed the first library by using link but have to do it
on the two others.
In my case, I even stop before pepXMLviewer and if I modify the
Makefile as written before, than I stop at PepXMLviewer.

Does anyone know how to fix that issue in the Makefile between 32 or
64 bit systems ?

Alex :o

On 21 sep, 17:13, "Greg Bowersock" <bowers...@gmail.com> wrote:
> Have you tried to make the changes that were mentioned in this thread:http://groups.google.com/group/spctools-discuss/browse_thread/thread/...

>
> The issues in that thread are most likely what is causing the problem.
>
> Greg
>

> > > > annotation issue (cygwin package ISB-MS-Tools-3.2-2e). Linux users

> > > - Show quoted text -- Masquer le texte des messages précédents -
>
> - Afficher le texte des messages précédents -

[Alex]

Hi Josh,

Works fine if you replace also the libs in the PepXMLviewer file as
such:

#
# cygwin or linux?
#
ifeq (${OS},Windows_NT)
OSFLAGS= -D__CYGWIN__

LDLIBS = libexpat.a -lboost_regex-gcc-mt-s -lboost_filesystem-gcc-mt-
s -lboost_serialization-gcc-mt-s #$(EXPAT)/.libs/libexpat.a
else
OSFLAGS= -D__LINUX__
# LDLIBS = libexpat.a /usr/lib/libboost_regex.a /usr/lib/
libboost_filesystem.a /usr/lib/libboost_serialization.a #$
(EXPAT)/.libs/libexpat.a
LDLIBS = libexpat.a -lboost_regex -lboost_filesystem -
lboost_serialization #$(EXPAT)/.libs/libexpat.a
endif

Perfect, no need to create link to those library to fool the system.

Cheers,

Alex

> > - Afficher le texte des messages précédents -- Hide quoted text -

[Joshua Tasman]

Dear SPC Tools Users,

We are releasing the next revision of the Trans-Proteomic Pipeline,

version 3.3.0 - SQUALL (cygwin package ISB-MS-Tools-3.3-0b). This

update includes many changes and improvements and all users are
recommended to update their software.

Some of the exciting changes in the TPP 3.3.0 release include:

o) The X!Tandem (with K-Score plugin) search engine is now integrated
into Petunia (the TPP GUI) to make using this open-source search engine
even easier; ISB/SPC default parameter files are installated;

o) PeptideProphet: addition of new retention-time model; updates to the
accurate mass and pI models; bugfix to deal with negative distributions;

o) ProteinProphet: correction to references multiple source input files;
fix to protein annotations;

o) Xpress: fix to apply fixed scan ranges to elution peaks from
command-line options;

o) Sqt2XML: fixed bug which duplicated first protein as alternative
protein; fixed search engine name: defaults to "SEQUEST", but will
override with "SQTGenerator" header entry; no longer writes
search_result element for a spectrum_query with no hits.

For downloading and installing the Windows version please visit the
following guide on our wiki:
"http://tools.proteomecenter.org/wiki/index.php?title=TPP:User_Documentation"

For downloading the source code, please go to the following link:
"http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=126912"

Everyone is encouraged to read and contribute to our wiki, at
http://tools.proteomecenter.org/wiki/

[Joshua Tasman]

There is a bug in the TPP v3.3.0 Cygwin installation involving the
gnuplot graphics package. Users are advised to avoid a clean install
until this is resolved tomorrow morning. Linux users are unaffected.

Apologies for the inconvenience,

Josh

[Alex]

Hey All,

Had to change the Makefile in mzXML/tools/readmzXML/ to avoid another
warning during compilation of 3.3.0 on 64 machine as such:
Replace: LDFLAGS= -L/usr/lib -L/usr/local/lib
With: LDFLAGS= -L/usr/lib64 -L/usr/local/lib64

I don't know what would be the right statement here to have it cope
with 32 or 64 machines?

Would it be possible to change the Makefiles for the next release so
that it works again on all systems ?

Cheers,

Alex

> > "http://tools.proteomecenter.org/wiki/index.php?title=TPP:User_Documen..."

>
> > For downloading the source code, please go to the following link:

> > "http://sourceforge.net/project/showfiles.php?group_id=69281&package_i..."

>
> > Everyone is encouraged to read and contribute to our wiki, at
> >http://tools.proteomecenter.org/wiki/
>

[Joshua Tasman]

A new TPP cygwin release, version 3.3.0c, resolves the recent graphics issues some of you may have
been experiencing. Please rerun the installer; Base->ISB-MS-Tools and Graphics->gnuplot should both
automatically update.

(This release also fixes an issue with webserver configuration related to the new retention time model.)

Linux users, please note that the svn release branch has been updated; if you compile from svn
source you'll want to make sure your version of gnuplot is updated to 4.2.

Please let us know of any graphics issues you encounter.

Thanks,

Josh, David, Luis

[jtasman]

An update to TPP version 3.3.0 for cygwin has been released: package
3.3.0d. This update should resolve the recent issues some of you may
have been experiencing with an unexpectedly large number of peptides or
proteins. Please rerun the installer; Base->ISB-MS-Tools should
automatically update to version 3.3.0d.

Linux users, please update from the SVN release_3-3-0 TPP branch.

Thanks,

Josh, David, Luis

[Joshua Tasman]

Dear SPC Tools Users,

We are releasing the next revision of the Trans-Proteomic Pipeline,

version 3.4.0 (cygwin package ISB-MS-Tools-3.4-0a). This

update includes many changes and improvements and all users are
recommended to update their software.

Note that this is the beginning of the 3.4.x series. See below ("new TPP
version numbering scheme") for more information.

Some significant changes that all users should be aware of:

o) based on user feedback and extensive testing from our collaborators at
LabKey, major changes to the prophet models have been implemented, including
improved behavior in cases in which a model was not reported in 3.3.0. Users
who saw negative changes in 3.3.0 should see improved results. See below for
more information.

o) Out2XML officially replaces out2summary and sequest2xml: this allows for
direct conversion of Sequest .out files to pepXML files. The older programs are
still included to allow users time to transition to the new system, but will be
removed in the next major release (3.5.0)

o) MzXML2Search officially replaced by MsXML2Other: MsXML2Other is no longer
distributed or supported.

o) runProphet script retired: this was an older wrapper around ProteinProphet
and has been retired. Command-line users should use ProteinProphet directly, or
xinteract.

o) new TPP version numbering scheme: 3.4.0 introduces a new numbering scheme.
.1 (minor) increments will introduce new features, while 0.0.1 increments will
denote any bug fixes that change results. Cygwin packages ('a', 'b', etc) will
only be updates for cygwin-only fixes (to the webserver, etc.)

other important changes:

o) PeptideProphet:
- important fixes to binning which should restore performance
- Nonparametric modeling
- optional 'ignore charge'
- optional 'force model' option to proceed even under bad distribution
separation cases

o) ProteinProphet:
- fixes for NSP model used when dynamic NSP model has too few bins

o) runsearch: uses Out2XML instead of retired out2summary

o) xinteract:
- Added -F (force the fitting of the mixture model),
-P (non-parametric model), and
-IX (Ignore Charge States) options for xinteract;

o) Petunia:
- Added Metabolic and Fixed Scan Range options for Xpress;
- Merge dynamic parameters into tandem xml input into new file, instead of
forcing users to use large-format parameters file as input;
- Allow users to choose a directory in File Chooser;
- Display current directory in tree view (File Browser);
- Feed dta2mzxml a directory/*.dta as input (to avoid extremely long input
arguments);
- Added -byname option for dta2mzxml;
- Replaced Sequest2XML with Out2XML in GUI-initiated processing
- Removed msxml2other from GUI
- Minor text and layout fixes.
- Re-added Maldi and Mass options for Out2XML; Updated Enzyme list drop-down
- Retire runprophet; call ProteinProphet directly

For downloading and installing the Windows version please visit the
following guide on our wiki:
"http://tools.proteomecenter.org/wiki/index.php?title=TPP:User_Documentation"

For downloading the source code, please go to the following link:
"http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=126912"
or directly from svn: see
http://sashimi.svn.sourceforge.net/svnroot/sashimi/tags/release_3-4-0

Everyone is encouraged to read and contribute to our wiki, at
http://tools.proteomecenter.org/wiki/

The SPC Tools team: David, Luis, Josh

[Joshua Tasman]

Dear SPC Tools Users,

We are releasing the next revision of the Trans-Proteomic Pipeline,

version 3.5.1 (cygwin package ISB-MS-Tools-3.5-1a). This

update includes many changes and improvements and all users are
recommended to update their software.

Note that this is the beginning of the 3.5.x series. (3.5.0 was an internal-only release.)

Some significant changes that all users should be aware of:

=TPP Version 3.5.0 Changes=

*significant PeptideProphet bug fixes and changes
*ASAPRatio: major bug fix
*file extension changes to .pep.xml and .prot.xml
*performance enhancements
*temporary TPP files cleaned up
*Tandem2XML
*xinteract: new prob 0 setting
*ProteinProphet: protein description reformatting
*Mascot2XML: parser fix
*major converter updates for ReAdW, wolf; introducing mzWiff (mzStar retired)

==significant PeptideProphet bug fixes and changes==

--bug fixes to allow modeling of ProbID using semi-supervised and semi-parameteric models
--bug fixes to allow semi-parameteric model to work with the force distribution and ignore charge options
--bug fix to correct computation of semi-parameteric model attributes (mean and stddev)
--bug fix to use the correct prior that includes the decoys when the DECOYPROBS option is used (ADVANCED OPTION: Use to test accuracy of program but not for final result reporting as selecting this option can make the probabilities inaccurate since it forces the program to assume that decoy matches are unknown when the final probabilities are calculated)
--(Re-)added max reward capping into PeptideProphet

=ASAPRatio: major bug fix==

ASAPRatioPeptideParser has been updated to correct an important bug: the previous version used modification masses specified in the pepXML file (which are average masses when fragment mass is selected to be average in the sequest.params file.) For high-mass accuracy instruments, where the monoisotopic mass should be used as the parent mass in the search parameters, ASAPRatio was ignoring the monoisotopic mass if specified on the command-line.
The updated version will correctly use the mass specified on the command-line. The command-line mass should be specified as the total monoisotopic mass of the modified amino acid(s).

This only affects high-mass-accuracy users who want to use a small window around the monoisotopic peak to detect the signal. If using default ASAPRatio parameters, this probably won't be an issue.

=file extension changes to .pep.xml and .prot.xml=
The default pepXML and protXML filename extensions are now “.pep.xml” and “.prot.xml” respectively, although older-style “.xml” and “-prot.xml” conventions still work seamlessly as input filenames. The existing commandline conventions for selecting output filenames are still there.

==performance enchancements==
Insilicos has folded in various performance enhancements from their retired IPP build of the sashimi tools.

==temporary TPP files cleaned up==

Tempfiles now all use generated unique names, so collisions between users should not be a problem (this was largely the case already, but not completely so).

CGI programs no longer leave temporary image files sitting around, they are deleted as soon as they are viewed. Also CGIs no longer try to clean up from previous runs by just deleting “*.png”.

==Tandem2XML==
Fix Tandem2XML to generate valid pepXML, even when "output, spectra" == "no". Turns out forcing this parameter yields something like 4x larger X! Tandem output, and it is killing the FHCRC. Also turns out, it is not that hard to fix.

6-digit precision for double values in Tandem2XML.

==xinteract: new prob 0 setting==
Fix xinteract to allow users to set prophet probability = 0 for both PeptideProphet and ProteinProphet.

==ProteinProphet: protein description reformatting==
The protein description string is written into protXML with spaces instead of pipes (vertical bars) in order
to make the HTML output tables less wide (and readable!)

==Mascot2XML parser fix==
Fixed parser error for modification data to consider parenthesis in name

==major converter updates for ReAdW, wolf; introducing mzWiff (mzStar retired)==
The official versions of ReAdW and wolf have been updated to version 3.5.1 with many changes.
mzWiff is a replacement for mzStar, and is much faster, more stable, and has more options.

Options for each converter can be found by running the programs with no arguments.

For downloading and installing the Windows version please visit the
following guide on our wiki:
"http://tools.proteomecenter.org/wiki/index.php?title=TPP:User_Documentation"

For downloading the source code, please go to the following link:
"http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=126912"

or directly from svn: see

http://sashimi.svn.sourceforge.net/svnroot/sashimi/tags/release_3-5-1

Everyone is encouraged to read and contribute to our wiki, at
http://tools.proteomecenter.org/wiki/

The SPC Tools team: Josh, Luis, David

[Joshua Tasman]

Dear SPC Tools Users,

We are releasing the next revision of the Trans-Proteomic Pipeline,

=TPP Version 3.5.0 Changes=

=ASAPRatio: major bug fix==

For downloading and installing the Windows version please visit the

following guide on our wiki:
"http://tools.proteomecenter.org/wiki/index.php?title=TPP:User_Documentation"

For downloading the source code, please go to the following link:
"http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=126912"

or directly from svn: see
http://sashimi.svn.sourceforge.net/svnroot/sashimi/tags/release_3-5-1

Everyone is encouraged to read and contribute to our wiki, at
http://tools.proteomecenter.org/wiki/

[Logan Everett]

I just upgraded by Windows/Cygwin based install to 3.5.1 and I'm no
longer able to use Tandem2XML on output.xml files that worked under
v3.4.x. The error I get now is: ERROR: Failed to open mzXML file.
The Tandem search was done on an MGF file, so there is no mzXML file
for me to give it. Is this related to the Tandem2XML fix that removes
the need for spectra in the output.xml file? Does this imply that all
tandem searches must be done with mzXML from now on in order to be
compatible with the TPP?

-Logan

[Ulrich auf dem Keller]

Hi all,

here are some notes for all folks out there who love to run the TPP natively on Mac OS X. Attached my Makefile.incl assuming boost and gd are installed via fink in /sw. For pwiz you have to add the following platform-dependent define to endian.hpp:

change from line 34:

#if (defined(PWIZ_GCC) && defined(__BYTE_ORDER) && __BYTE_ORDER==__LITTLE_ENDIAN) || \

    (defined(__MINGW32__)) || \

    (defined(PWIZ_MSVC) && defined(_M_IX86))

#define PWIZ_LITTLE_ENDIAN

#endif

to:

#if (defined(PWIZ_GCC) && defined(__BYTE_ORDER) && __BYTE_ORDER==__LITTLE_ENDIAN) || \

    (defined(__MINGW32__)) || \

    (defined(__i386__)) || \

    (defined(PWIZ_MSVC) && defined(_M_IX86))

#define PWIZ_LITTLE_ENDIAN

#endif

Also change the dta2mzxml Makefile and add to the LDLIBS and IFLAGS entries:

LDLIBS = -L/sw/lib -lboost_filesystem 

IFLAGS += -I../../common -I/sw/include/

With these changes the TPP should compile fine (assuming all dependencies are installed (see wiki)). 

During "make install" I recognized that somehow the dta2mzxml binary is not copied to the new linux/build directory. Therefore, you should do that manually before running "make install".

For the future it might be possible to add an extra section for ARCH = darwin to Makefile.incl. Thanks a lot to the developers to enhance platform-compatibility of the TPP source!!

Cheers,

Ulrich

[Joshua Tasman]

Excellent work, Ulrich!

-Josh

> =
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> Dr. Ulrich auf dem Keller
> Overall Lab
> Centre for Bl*oo*d Research
> University of British Columbia
> Life Sciences Centre
> #4.420 - 2350 Health Sciences Mall
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> Tel.: 604-822-3561
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[jtasman]

Dear SPC Tools Users,

The Trans-Proteomic Pipeline 3.5.x series has been updated with the
release of version 3.5.2 (cygwin package ISB-MS-Tools-3.5-2a). This
update includes many changes and improvements and all 3.5.x users are
encouraged to update.

=TPP Version 3.5.2 Changes=

*converters: memory leak fixes corrected
ReAdW, wolf, and mzWiff had memory leaks that could accumulate if run
many times on the same machine. Special thanks to Dmitrii Tchekhovskoi
to catching and patching these bugs

*ReAdW and wolf: stricter options checking
The programs now correctly catch mis-formed arguments

*ReAdW: handling TSQ MRM data

*Mascot2XML: fix to handle yet another scan number description variant
("ScanNumber=xxx")

*Tandem2XML: as this program no longer processes MGF search results,
warn instead of error when mzXML file not found.

*calctppstat.pl: this helpful script which generates statistics on TPP
results has been updated (found in TPP/testing in source code.)

For downloading and installing the Windows version please visit the
following guide on our wiki:
"http://tools.proteomecenter.org/wiki/index.php?title=TPP:User_Documentation"

For downloading the source code, please go to the following link:
"http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=126912"

or directly from svn: see

http://sashimi.svn.sourceforge.net/svnroot/sashimi/tags/release_3-5-2
Please refer to the readme file in TPP/src as well as the wiki.

Everyone is encouraged to read and contribute to our wiki, at
http://tools.proteomecenter.org/wiki/

[Joshua Tasman]

For those who have yet to install 3.5.2, we will release another update in the near future (within the next 24 hours), so you might want to hold off.

Apologies for any inconvenience for the early adopters,

Josh

[Joshua Tasman]

TPP 3.5.3 has been released. Please see spctools-announce for the full release notes.

[Josh T]

A major bug has been discovered in the latest release (3.5.3). For
those who use ASAPRatio, updating ASAPRatio results through the web
interface will *delete* the corresponding pepXML file.
Please check any files you have tried to update in the recent past.

An update will be made as soon as this is resolved.

-Josh

[Brian Pratt]

Actually this isn't a problem unless you have specified a WEBSERVER_TMP
environment variable for your webserver, *and* it specifies a directory for
your tempfiles which is on a different volume than your result files. So
for pretty much everyone using TPP this is a non-event.

- Brian

[Joshua Tasman]

And, it turns out that our problem was due to some corrupted data files on our machine here at the ISB, so nothing to worry about.

Josh

[Joshua Tasman]

TPP 3.5.4 has been released. Please see spctools-announce for the full release notes.

The SPC Tools team: Josh, David, Luis

[Greg Bowersock]

It looks like there is a bug during installation if you are compiling under linux. I created a Makefile.config.incl as directed by the Makefile.incl, and everything compiled just fine. However, during installation the installation crashed when it tried to copy the help files. It tried to use the default path, instead of the path defined in the Makefile.config.incl file. I just hacked the Makefile.incl to make it work, but I'm, wondering if SRC_ROOT needs to be included in the Makefile in HELP_DIR, since it is not under the src directory (there is a note in the Makefile.incl mentioning something to that effect).

 

Greg
 

[Brian Pratt]

Just to clarify for everyone, this is NOT an issue with the new release, it’s an issue with the unreleased code that’s under development.  If you speak geek, the release is built with a “branch” of the code, and the build issue Greg is encountering is only in the developmental “trunk” of the code.  Working with trunk gets you the latest and greatest the project has to offer, along with the occasional poke in the eye – such is the joy and pain of open source software.

 

OK, so:

 

Hi Greg,

 

The Makefile.config.incl stuff is new, and it’s probably just not yet as general as it needs to be.  Can you post the contents of your Makefile.config.incl so I can see what the matter might be?  It would also be instructive to see your hacked Makefile.incl, too (although the idea, obviously, was to get away from making folks hack a file that’s under source control).

 

Thanks,

 

Brian

 

---

<br

[Greg Bowersock]

Sorry about that confusion, I didn't thank about that. I wondered why I hadn't noticed a mention of the new file when Josh announced the new version. :)

 

Makefile.config.incl:

 

#
# Makefile.config.incl
TPP_ROOT=/home/TPP/tpp/
 

 

And the only change I made to the Makefile.incl file was changing:

ifeq ($(strip $(TPP_ROOT)),)
# don't edit here, create Makefile.config.incl instead
TPP_ROOT=/usr/local/tpp/
endif

 

to:

ifeq ($(strip $(TPP_ROOT)),)
# don't edit here, create Makefile.config.incl instead
TPP_ROOT=/home/TPP/tpp/
endif


 

[Brian Pratt]

No worries. Grab fresh code and it should work now – I had missed a handful of installation related makefiles.  I’ve added some safeguards against anyone repeating my error in future, as well.

<br