TPP:4.7.1 Release Notes

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Current revision

Trans-Proteomic Pipeline (TPP) software, release 4.7.1 is a maintenance release of TPP that contains changes to 4.7.0. 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 users are recommended to use the Windows installer, which installs and configures the TPP and other required software (such as a web server). For advanced users who need to customize the TPP, or for those who run high-throughput experiments, you can download the source code. Again, most users don't need build from source, and should use the Windows installer.

Previous release notes are available at TPP:4.7.0_Release_Notes

1 New Features
2 Improvements/Changes
3 Bug fixes
4 Miscellaneous
5 Known Issues
6 Getting the TPP Software
7 SVN Log

[edit]

New Features

CGI/show_tmp_pngfile.pl: added option to keep the png file...show and not delete

iProphet: Rewrite spectrum_query index to make unique for quantitation tools.

ASAPRatio: Use iProphet probs if present. When running gnuplot test for existence of the png file image before deleting the temporaries.

Petunia (iProphet Page): Add an option to launch ProteinProphet,
- iProphet Page in Petunia can now run PTMProphet and Quantitation Tools.

[edit]

Improvements/Changes

Upgraded Comet to 2014.01 rev. 0

Petunia:
- Made Comet the default search engine; added a link to its project page
- Removed (rarely used) advanced options for ProteinProphet in xinteract page
- Added new (default) option of PPM units for AccMass model; also moved this oft-used option to the top
- Added link to Mayu project page
- Added 'no spaces' validation for filepaths and other parameters
- Made sure iProphet page actually catches errors
- Added warning if speclibs dir does not exist
- Added option to report probs for decoy hits in PeptideProphet
- Change 'Paste' button color after click to indicate it is working.
- Minor formatting and CSS changes

PlotSpectraST:
- Added support for mzML

ProtXMLViewer
- Added ability to view all entries connected to a peptide sequence, accessed via the peptide weight link (obviates prot_wt_xml.pl)
- Added peptide/spectrum links to PepXMLViewer (obviates peptidexml_html2.pl)
- Added links to ASAPRatio and XPRESS protein curation interfaces, plus sort/filter controls
- Added option to view/filter/sort pvalue-adjusted ASAPRatio values
- Report number of single hits (as determined by number of spectra assigned to a protein)
- Streamlined decoy highlighting code
- Attempt to run tpp_models if no MODELS file found
- Added simple export to TSV/Excel (via AJAX call)

[edit]

Bug fixes

Fixed the "blank" page presented in Petunia when using basic authentication and you happen to open the main URL without any actions

Corrected an issue with Sqt2XML that resulted in a incomplete pep.xml file when the -r option is not used. The -r option now defaults to 10.

[X!Tandem] fixed broken modification parsing; suppress warning messages for duplicate mods

Corrected an issue when building TPP on linux where the variable PERL_BIN was getting set later in the perl_paths rule, which means ESCAPED_PERL_BIN then is always empty and the resulting TPP didn't know where the perl executable was.

PepXMLViewer.cgi: MZRatio is reported as a link only in html mode now, simple value every other mode.

iProphet: Fix FPKM message bug.

Sqt2XML: fix bug when empty lines happen in an Sqt, don't quit..skip to next spectrum_query, reported on spctools-discuss

tpp_gui.pl: fix bug with deleted pepXMLs on windows when using unmerged analysis in runXinteract, cleaner auto-naming scheme for runXinteract.

correct time reporting in xinteract -D_USE_32BIT_TIME_T

ASAPRatioPeptideParser: Undo change that broke -r option

iModelParser.cgi: fixing memory issue exposed under MingW
- iModelParser.cgi: fill in correct value for score.

Set the default gnuplot binary to point to pgnuplot.exe on windows.

[edit]

Miscellaneous

No known issues to report

[edit]

Known Issues

Spectrast (and presumably other TPP programs) have a 2 GB file limit on Windows due to the use of C++ fstreams and the 32-bit libraries they are linked against.

Compile errors in Boost have been reported on the spctools mailing list with recent versions of Ubuntu. The following patch appears to resolve the issue: https://svn.boost.org/trac/boost/changeset/84950#file0

[edit]

Getting the TPP Software

Download the TPP version 4.7.1 native windows installer (TPP_Setup_v4_7_1.exe) from the Sashimi SourceForge project file release page:

 http://sourceforge.net/projects/sashimi/files/

Everyone is encouraged to read and contribute to our wiki, at

 http://tools.proteomecenter.org/wiki/

For guides to installing and using our software, please see our wiki:

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

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

 http://sourceforge.net/projects/sashimi/files/ and find the 4.7.1 source code .tgz package;

Or, check out the code directly from svn:

 svn checkout svn://svn.code.sf.net/p/sashimi/code/tags/release_4-7-1

For building from source, please refer to the readme file in TPP/src as well as the wiki.

The TPP Team: Luis, David, Mike, Joe, and Jimmy plus all other developers who contributed to this release from the ISB. Thanks to developers and users from the TPP's user community who provided feedback and code contributions.

[edit]

SVN Log

The SVN log of all changes since the previous release are available at TPP:4.7.1_SVN_Log.

Retrieved from "http://tools.proteomecenter.org/wiki/index.php?title=TPP:4.7.1_Release_Notes"

-'''***** DRAFT *****'''
 Trans-Proteomic Pipeline (TPP) software, release 4.7.1 is a maintenance release of TPP that contains changes to 4.7.0.  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 users are recommended to use the Windows installer, which installs and configures the TPP and other required software (such as a web server).  For advanced users who need to customize the TPP, or for those who run high-throughput experiments, you can download the source code.  Again, most users don't need build from source, and should use the Windows installer.
 == New Features ==
-* something something something
+* CGI/show_tmp_pngfile.pl:  added option to keep the png file...show and not delete
+* iProphet:  Rewrite spectrum_query index to make unique for quantitation tools.
+* ASAPRatio: Use iProphet probs if present. When running gnuplot test for existence of the png file image before deleting the temporaries.
+* Petunia (iProphet Page):  Add an option to launch ProteinProphet,
+** iProphet Page in Petunia can now run PTMProphet and Quantitation Tools.
 == Improvements/Changes ==
-* otherotherother
+* Upgraded ''Comet'' to 2014.01 rev. 0
+* ''Petunia'':
+** Made ''Comet'' the default search engine; added a link to its project page
+** Removed (rarely used) advanced options for ProteinProphet in xinteract page
+** Added new (default) option of PPM units for AccMass model; also moved this oft-used option to the top
+** Added link to Mayu project page
+** Added 'no spaces' validation for filepaths and other parameters
+** Made sure iProphet page actually catches errors
+** Added warning if speclibs dir does not exist
+** Added option to report probs for decoy hits in PeptideProphet
+** Change 'Paste' button color after click to indicate it is working.
+** Minor formatting and CSS changes
+* ''PlotSpectraST'':
+** Added support for mzML
+* ''ProtXMLViewer''
+** Added ability to view all entries connected to a peptide sequence, accessed via the peptide weight link (obviates ''prot_wt_xml.pl'')
+** Added peptide/spectrum links to ''PepXMLViewer'' (obviates ''peptidexml_html2.pl'')
+** Added links to ''ASAPRatio'' and ''XPRESS'' protein curation interfaces, plus sort/filter controls
+** Added option to view/filter/sort ''pvalue''-adjusted ASAPRatio values
+** Report number of single hits (as determined by number of spectra assigned to a protein)
+** Streamlined decoy highlighting code
+** Attempt to run ''tpp_models'' if no MODELS file found
+** Added simple export to TSV/Excel (via AJAX call)
 == Bug fixes ==
-* no bugs here
+* Fixed the "blank" page presented in Petunia when using basic authentication and you happen to open the main URL without any actions
+* Corrected an issue with Sqt2XML that resulted in a incomplete pep.xml file when the -r option is not used.  The -r option now defaults to 10.
+* [X!Tandem] fixed broken modification parsing; suppress warning messages for duplicate mods
+* Corrected an issue when building TPP on linux where the variable PERL_BIN was getting set later in the perl_paths rule, which means ESCAPED_PERL_BIN then is always empty and the resulting TPP didn't know where the perl executable was.
+* PepXMLViewer.cgi: MZRatio is reported as a link only in html mode now, simple value every other mode.
+* iProphet:  Fix FPKM message bug.
+* Sqt2XML: fix bug when empty lines happen in an Sqt, don't quit..skip to next spectrum_query, reported on spctools-discuss
+* tpp_gui.pl: fix bug with deleted pepXMLs on windows when using unmerged analysis in runXinteract,  cleaner auto-naming scheme for runXinteract.
+* correct time reporting in xinteract -D_USE_32BIT_TIME_T
+* ASAPRatioPeptideParser: Undo change that broke -r option
+* iModelParser.cgi: fixing memory issue exposed under MingW
+** iModelParser.cgi: fill in correct value for score.
+* Set the default gnuplot binary to point to pgnuplot.exe on windows.
 == Miscellaneous ==
 == Known Issues ==
-* ''No known issues to report''
+* Spectrast (and presumably other TPP programs) have a 2 GB file limit on Windows due to the use of C++ fstreams and the 32-bit libraries they are linked against.
+* Compile errors in Boost  have been reported on the spctools mailing list with recent versions of Ubuntu.  The following patch appears to resolve the issue: https://svn.boost.org/trac/boost/changeset/84950#file0
 == Getting the TPP Software ==
 * For downloading the source code, please go to the following link:
   http://sourceforge.net/projects/sashimi/files/ and find the 4.7.1 source code .tgz package;
-or, check out the code directly from svn:
+* Or, check out the code directly from svn:
   svn checkout svn://svn.code.sf.net/p/sashimi/code/tags/release_4-7-1
-** For building from source, please refer to the readme file in TPP/src as well as the wiki.
+* For building from source, please refer to the readme file in TPP/src as well as the wiki.
 The TPP Team: Luis, David, Mike, Joe, and Jimmy plus all other developers who contributed to this release from the ISB.  Thanks to developers and users from the TPP's user community who provided feedback and code contributions.

TPP:4.7.1 Release Notes

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SVN Log

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